diff --git a/apps/staged/src/lib/features/branches/BranchCard.svelte b/apps/staged/src/lib/features/branches/BranchCard.svelte
index 3aab3563..e16fdffe 100644
--- a/apps/staged/src/lib/features/branches/BranchCard.svelte
+++ b/apps/staged/src/lib/features/branches/BranchCard.svelte
@@ -19,6 +19,7 @@
   import type {
     Branch,
     BranchTimeline as BranchTimelineData,
+    ProjectRepo,
     SessionStatusPayload,
     WorkspaceStatus,
   } from '../../types';
@@ -43,7 +44,7 @@
 
   interface Props {
     branch: Branch;
-    repoLabel?: { githubRepo: string; subpath: string | null; reason?: string | null } | null;
+    repoLabel?: ProjectRepo | null;
     projectName?: string;
     deleting?: boolean;
     worktreeError?: string;
@@ -52,6 +53,7 @@
     onRename?: (branchName: string) => void;
     onRetryWorktree?: () => void;
     onWorkspaceStatusChange?: (status: WorkspaceStatus, workstationId?: number | null) => void;
+    onDismissReason?: (projectRepoId: string) => void;
   }
 
   let {
@@ -65,6 +67,7 @@
     onRename,
     onRetryWorktree,
     onWorkspaceStatusChange,
+    onDismissReason,
   }: Props = $props();
 
   // Determine if this is a local or remote branch
@@ -521,6 +524,7 @@
     if (branch.projectRepoId) {
       try {
         await commands.clearProjectRepoReason(branch.projectRepoId);
+        onDismissReason?.(branch.projectRepoId);
       } catch (e) {
         console.error('Failed to clear repo reason:', e);
       }
diff --git a/apps/staged/src/lib/features/branches/BranchCardActionsBar.svelte b/apps/staged/src/lib/features/branches/BranchCardActionsBar.svelte
index af00398f..ad1f6d44 100644
--- a/apps/staged/src/lib/features/branches/BranchCardActionsBar.svelte
+++ b/apps/staged/src/lib/features/branches/BranchCardActionsBar.svelte
@@ -30,7 +30,7 @@
   import SineWave from '../../shared/SineWave.svelte';
   import ActionOutputModal from '../actions/ActionOutputModal.svelte';
   import { listen, type UnlistenFn } from '@tauri-apps/api/event';
-  import type { Branch } from '../../types';
+  import type { Branch, ProjectRepo } from '../../types';
   import * as commands from '../../api/commands';
   import type { ProjectAction } from '../../api/commands';
   import {
@@ -58,7 +58,7 @@
 
   interface Props {
     branch: Branch;
-    repoLabel?: { githubRepo: string; subpath: string | null; reason?: string | null } | null;
+    repoLabel?: ProjectRepo | null;
     isLocal: boolean;
     isRemote: boolean;
     remoteWorkspaceStatus: string | null;
diff --git a/apps/staged/src/lib/features/branches/BranchCardHeaderInfo.svelte b/apps/staged/src/lib/features/branches/BranchCardHeaderInfo.svelte
index 2a766f0f..3f9a0f07 100644
--- a/apps/staged/src/lib/features/branches/BranchCardHeaderInfo.svelte
+++ b/apps/staged/src/lib/features/branches/BranchCardHeaderInfo.svelte
@@ -1,10 +1,11 @@
 <script lang="ts">
   import { GitBranch } from 'lucide-svelte';
   import RepoLabel from '../../shared/RepoLabel.svelte';
+  import type { ProjectRepo } from '../../types';
 
   interface Props {
     branchName: string;
-    repoLabel?: { githubRepo: string; subpath: string | null } | null;
+    repoLabel?: ProjectRepo | null;
     secondaryLabel?: string | null;
   }
 
diff --git a/apps/staged/src/lib/features/projects/ProjectHome.svelte b/apps/staged/src/lib/features/projects/ProjectHome.svelte
index 2ab87476..eea84b46 100644
--- a/apps/staged/src/lib/features/projects/ProjectHome.svelte
+++ b/apps/staged/src/lib/features/projects/ProjectHome.svelte
@@ -8,7 +8,13 @@
   import { onMount } from 'svelte';
   import { getCurrentWindow } from '@tauri-apps/api/window';
   import { listen, type UnlistenFn } from '@tauri-apps/api/event';
-  import type { Project, Branch, StoreIncompatibility, WorkspaceStatus } from '../../types';
+  import type {
+    Project,
+    ProjectRepo,
+    Branch,
+    StoreIncompatibility,
+    WorkspaceStatus,
+  } from '../../types';
   import * as commands from '../../api/commands';
   import { listenToRepoActionsDetection } from '../actions/actions';
   import { projectDisplayName } from '../../shared/utils';
@@ -32,9 +38,17 @@
   // Data
   let projects = $state<Project[]>([]);
   let branchesByProject = $state<Map<string, Branch[]>>(new Map());
-  let repoLabelsByProject = $state<
-    Map<string, Map<string, { githubRepo: string; subpath: string | null; reason: string | null }>>
-  >(new Map());
+  let reposById = $state<Map<string, ProjectRepo>>(new Map());
+
+  /** Replace all cached repos for a single project with a fresh list. */
+  function replaceProjectRepos(projectId: string, repos: ProjectRepo[]) {
+    const next = new Map(reposById);
+    for (const [id, repo] of next) {
+      if (repo.projectId === projectId) next.delete(id);
+    }
+    for (const repo of repos) next.set(repo.id, repo);
+    reposById = next;
+  }
   let loading = $state(true);
   let error = $state<string | null>(null);
   let loadGeneration = 0;
@@ -109,22 +123,7 @@
         projects = projectsList;
         branchesByProject = new Map(branchesByProject).set(projectId, branches);
         workspaceLifecycle.enqueueInitialSetup(projectId, branches);
-        repoLabelsByProject = new Map(repoLabelsByProject).set(
-          projectId,
-          new Map(
-            repos.map(
-              (repo) =>
-                [
-                  repo.id,
-                  {
-                    githubRepo: repo.githubRepo,
-                    subpath: repo.subpath ?? null,
-                    reason: repo.reason ?? null,
-                  },
-                ] as const
-            )
-          )
-        );
+        replaceProjectRepos(projectId, repos);
       } catch (e) {
         console.error('[ProjectHome] Failed to refresh project after setup progress:', e);
       }
@@ -222,16 +221,18 @@
 
       // Seed maps so project sections can render immediately.
       const branchMap = new Map<string, Branch[]>();
-      const repoLabelMap = new Map<
-        string,
-        Map<string, { githubRepo: string; subpath: string | null; reason: string | null }>
-      >();
       for (const project of projectList) {
         branchMap.set(project.id, branchesByProject.get(project.id) || []);
-        repoLabelMap.set(project.id, repoLabelsByProject.get(project.id) || new Map());
       }
       branchesByProject = branchMap;
-      repoLabelsByProject = repoLabelMap;
+
+      // Drop cached repos for projects that no longer exist.
+      const projectIds = new Set(projectList.map((p) => p.id));
+      const prunedRepos = new Map<string, ProjectRepo>();
+      for (const [id, repo] of reposById) {
+        if (projectIds.has(repo.projectId)) prunedRepos.set(id, repo);
+      }
+      reposById = prunedRepos;
 
       await Promise.all(
         projectList.map(async (project) => {
@@ -243,22 +244,7 @@
             if (generation !== loadGeneration) return;
             branchesByProject = new Map(branchesByProject).set(project.id, branches);
             workspaceLifecycle.enqueueInitialSetup(project.id, branches);
-            repoLabelsByProject = new Map(repoLabelsByProject).set(
-              project.id,
-              new Map(
-                repos.map(
-                  (repo) =>
-                    [
-                      repo.id,
-                      {
-                        githubRepo: repo.githubRepo,
-                        subpath: repo.subpath ?? null,
-                        reason: repo.reason ?? null,
-                      },
-                    ] as const
-                )
-              )
-            );
+            replaceProjectRepos(project.id, repos);
           } catch (e) {
             console.error(`[ProjectHome] Failed to hydrate project '${project.id}':`, e);
           }
@@ -303,7 +289,10 @@
   let repoCountsByProject = $derived(
     new Map(
       projects.map((project) => {
-        const knownCount = repoLabelsByProject.get(project.id)?.size ?? 0;
+        let knownCount = 0;
+        for (const repo of reposById.values()) {
+          if (repo.projectId === project.id) knownCount++;
+        }
         const fallbackCount = project.githubRepo ? 1 : 0;
         return [project.id, knownCount > 0 ? knownCount : fallbackCount] as const;
       })
@@ -385,22 +374,7 @@
     ]);
     branchesByProject = new Map(branchesByProject).set(project.id, branches);
     workspaceLifecycle.enqueueInitialSetup(project.id, branches);
-    repoLabelsByProject = new Map(repoLabelsByProject).set(
-      project.id,
-      new Map(
-        repos.map(
-          (repo) =>
-            [
-              repo.id,
-              {
-                githubRepo: repo.githubRepo,
-                subpath: repo.subpath ?? null,
-                reason: repo.reason ?? null,
-              },
-            ] as const
-        )
-      )
-    );
+    replaceProjectRepos(project.id, repos);
     showNewProjectModal = false;
     selectProject(project.id);
   }
@@ -469,9 +443,11 @@
       const nextBranches = new Map(branchesByProject);
       nextBranches.delete(id);
       branchesByProject = nextBranches;
-      const nextRepoLabels = new Map(repoLabelsByProject);
-      nextRepoLabels.delete(id);
-      repoLabelsByProject = nextRepoLabels;
+      const nextRepos = new Map(reposById);
+      for (const [repoId, repo] of nextRepos) {
+        if (repo.projectId === id) nextRepos.delete(repoId);
+      }
+      reposById = nextRepos;
       for (const branch of branchesToClear) {
         workspaceLifecycle.clearBranchState(branch.id);
       }
@@ -515,22 +491,7 @@
       projects = projectsList;
       branchesByProject = new Map(branchesByProject).set(projectId, branches);
       workspaceLifecycle.enqueueInitialSetup(projectId, branches);
-      repoLabelsByProject = new Map(repoLabelsByProject).set(
-        projectId,
-        new Map(
-          repos.map(
-            (repo) =>
-              [
-                repo.id,
-                {
-                  githubRepo: repo.githubRepo,
-                  subpath: repo.subpath ?? null,
-                  reason: repo.reason ?? null,
-                },
-              ] as const
-          )
-        )
-      );
+      replaceProjectRepos(projectId, repos);
     } catch (e) {
       console.error('Failed to add repo:', e);
       const message = e instanceof Error ? e.message : String(e);
@@ -612,22 +573,7 @@
         ]);
         projects = projectsList;
         branchesByProject = new Map(branchesByProject).set(branch.projectId, branches);
-        repoLabelsByProject = new Map(repoLabelsByProject).set(
-          branch.projectId,
-          new Map(
-            repos.map(
-              (repo) =>
-                [
-                  repo.id,
-                  {
-                    githubRepo: repo.githubRepo,
-                    subpath: repo.subpath ?? null,
-                    reason: repo.reason ?? null,
-                  },
-                ] as const
-            )
-          )
-        );
+        replaceProjectRepos(branch.projectId, repos);
       } else {
         await commands.deleteBranch(branch.id);
         // Fallback for legacy branches without repo linkage
@@ -733,7 +679,7 @@
           <ProjectSection
             {project}
             branches={branchesByProject.get(project.id) || []}
-            repoLabelsById={repoLabelsByProject.get(project.id) || new Map()}
+            {reposById}
             canAddRepo={canAddRepo(project)}
             addRepoHint={project.location === 'remote' ? addRepoHint(project) : null}
             deleting={deletingProjectNames.has(project.id)}
@@ -749,10 +695,18 @@
             onWorkspaceStatusChange={(branchId, workspaceStatus, workstationId) =>
               handleWorkspaceStatusChange(project.id, branchId, workspaceStatus, workstationId)}
             excludeRepos={new Set(
-              [...(repoLabelsByProject.get(project.id)?.values() ?? [])].map((r) => r.githubRepo)
+              [...reposById.values()]
+                .filter((r) => r.projectId === project.id)
+                .map((r) => r.githubRepo)
             )}
             onRepoSelected={(selection) => handleRepoSelected(project.id, selection)}
             onRetryWorktree={(branchId) => setupBranchWorktree(branchId, project.id)}
+            onDismissReason={(projectRepoId) => {
+              const repo = reposById.get(projectRepoId);
+              if (repo) {
+                reposById = new Map(reposById).set(projectRepoId, { ...repo, reason: null });
+              }
+            }}
           />
         {/each}
       </div>
diff --git a/apps/staged/src/lib/features/projects/ProjectSection.svelte b/apps/staged/src/lib/features/projects/ProjectSection.svelte
index f3c25c90..dec6bb45 100644
--- a/apps/staged/src/lib/features/projects/ProjectSection.svelte
+++ b/apps/staged/src/lib/features/projects/ProjectSection.svelte
@@ -22,7 +22,7 @@
     X,
     ImagePlus,
   } from 'lucide-svelte';
-  import type { Project, Branch, WorkspaceStatus, ProjectNote } from '../../types';
+  import type { Project, ProjectRepo, Branch, WorkspaceStatus, ProjectNote } from '../../types';
   import { projectDisplayName } from '../../shared/utils';
   import { goHome } from '../layout/navigation.svelte';
   import * as commands from '../../api/commands';
@@ -45,10 +45,7 @@
   interface Props {
     project: Project;
     branches: Branch[];
-    repoLabelsById?: Map<
-      string,
-      { githubRepo: string; subpath: string | null; reason: string | null }
-    >;
+    reposById?: Map<string, ProjectRepo>;
     canAddRepo?: boolean;
     addRepoHint?: string | null;
     deleting?: boolean;
@@ -68,12 +65,13 @@
     ) => void;
     onRepoSelected?: (selection: RepoPickerSelection) => void;
     onRetryWorktree?: (branchId: string) => void;
+    onDismissReason?: (projectRepoId: string) => void;
   }
 
   let {
     project,
     branches,
-    repoLabelsById = new Map(),
+    reposById = new Map(),
     canAddRepo = true,
     addRepoHint = null,
     deleting = false,
@@ -89,6 +87,7 @@
     onWorkspaceStatusChange,
     onRepoSelected,
     onRetryWorktree,
+    onDismissReason,
   }: Props = $props();
 
   let sortedBranches = $derived([...branches].sort((a, b) => b.createdAt - a.createdAt));
@@ -159,14 +158,9 @@
     return () => window.removeEventListener('pointerdown', onPointerDown);
   });
 
-  function repoLabelForBranch(
-    branch: Branch
-  ): { githubRepo: string; subpath: string | null } | null {
-    const fallback = project.githubRepo
-      ? { githubRepo: project.githubRepo, subpath: project.subpath ?? null }
-      : null;
-    if (!branch.projectRepoId) return fallback;
-    return repoLabelsById.get(branch.projectRepoId) ?? fallback;
+  function repoForBranch(branch: Branch): ProjectRepo | null {
+    if (!branch.projectRepoId) return null;
+    return reposById.get(branch.projectRepoId) ?? null;
   }
 
   // ── Project session input ──────────────────────────────────────────────
@@ -634,7 +628,7 @@
     {#each sortedBranches as branch (branch.id)}
       <BranchCard
         {branch}
-        repoLabel={repoLabelForBranch(branch)}
+        repoLabel={repoForBranch(branch)}
         projectName={project.name}
         deleting={deletingBranches.has(branch.id)}
         worktreeError={worktreeErrors.get(branch.id)}
@@ -644,6 +638,7 @@
         onRetryWorktree={() => onRetryWorktree?.(branch.id)}
         onWorkspaceStatusChange={(status, workstationId) =>
           onWorkspaceStatusChange?.(branch.id, status, workstationId)}
+        {onDismissReason}
       />
     {/each}
   </div>