diff --git a/src/lib/components/Sidebar.svelte b/src/lib/components/Sidebar.svelte
index 22b55fe..7890d9e 100644
--- a/src/lib/components/Sidebar.svelte
+++ b/src/lib/components/Sidebar.svelte
@@ -83,6 +83,23 @@
     return true;
   }
 
+  // `refActionsBlocked()` only covers the instant of the click. Every ref action that asks
+  // first then waits on a prompt with no timeout, during which the repository can change —
+  // and `gitActions` targets `appState.repo`, not whatever was on screen when the dialog
+  // opened. Confirming afterwards would run the OLD repo's branch or tag name against the
+  // NEW repository; where both hold that name, "Delete" force-deletes the wrong one.
+  //
+  // Capture the repo before the await and re-check after it. Returns a predicate rather than
+  // taking a callback so each call site keeps its own control flow readable.
+  function sameRepoAfterPrompt(): () => boolean {
+    const opened = appState.repo;
+    return () => {
+      if (appState.repo === opened) return true;
+      appState.status = "Repository changed while that dialog was open — nothing was done.";
+      return false;
+    };
+  }
+
   function onRefCheckout(r: RefEntry, kind: "local" | "remote" | "tag") {
     if (refActionsBlocked()) return;
     if (kind === "local") {
@@ -108,8 +125,9 @@
     const upstream = remoteExists ? tracking : null;
     const remoteGone = tracking !== null && !remoteExists;
     const worktree = worktreeFor(name) ?? null;
+    const sameRepo = sameRepoAfterPrompt();
     const res = await dialogs.confirmBranchDelete({ branch: name, upstream, remoteGone, worktree });
-    if (!res.confirmed) return;
+    if (!res.confirmed || !sameRepo()) return;
     let remote: string | undefined;
     let remoteBranch: string | undefined;
     if (res.deleteRemote && upstream) {
@@ -175,15 +193,17 @@
       items.push({
         label: "Rename…",
         action: async () => {
+          const sameRepo = sameRepoAfterPrompt();
           const n = await dialogs.prompt({ title: "Rename branch", label: "New name", value: r.name });
-          if (n && n !== r.name) gitActions.renameBranch(r.name, n);
+          if (n && n !== r.name && sameRepo()) gitActions.renameBranch(r.name, n);
         },
       });
       items.push({
         label: "Create tag here…",
         action: async () => {
+          const sameRepo = sameRepoAfterPrompt();
           const n = await dialogs.prompt({ title: "New tag", label: "Tag name", placeholder: "v1.0.0" });
-          if (n) gitActions.createTag(n, r.sha);
+          if (n && sameRepo()) gitActions.createTag(n, r.sha);
         },
       });
       items.push({ separator: true });
@@ -193,8 +213,9 @@
       items.push({
         label: "Create local branch…",
         action: async () => {
+          const sameRepo = sameRepoAfterPrompt();
           const n = await dialogs.prompt({ title: `New branch from ${r.name}`, label: "Branch name" });
-          if (n) gitActions.createBranch(n, r.sha);
+          if (n && sameRepo()) gitActions.createBranch(n, r.sha);
         },
       });
       items.push({ separator: true });
@@ -205,13 +226,14 @@
           const slash = r.name.indexOf("/");
           const remote = r.name.slice(0, slash);
           const branch = r.name.slice(slash + 1);
+          const sameRepo = sameRepoAfterPrompt();
           const ok = await dialogs.confirm({
             title: "Delete remote branch",
             message: `Delete "${r.name}" on the remote? This removes it for everyone with access to ${remote}.`,
             confirmLabel: "Delete",
             danger: true,
           });
-          if (ok) gitActions.deleteRemoteBranch(remote, branch);
+          if (ok && sameRepo()) gitActions.deleteRemoteBranch(remote, branch);
         },
       });
     } else {
@@ -221,13 +243,14 @@
         label: "Delete tag",
         danger: true,
         action: async () => {
+          const sameRepo = sameRepoAfterPrompt();
           const ok = await dialogs.confirm({
             title: "Delete tag",
             message: `Delete tag "${r.name}"?`,
             confirmLabel: "Delete",
             danger: true,
           });
-          if (ok) gitActions.deleteTag(r.name);
+          if (ok && sameRepo()) gitActions.deleteTag(r.name);
         },
       });
     }
@@ -264,8 +287,9 @@
       {
         label: "Create branch here…",
         action: async () => {
+          const sameRepo = sameRepoAfterPrompt();
           const n = await dialogs.prompt({ title: `New branch at ${sha.slice(0, 7)}`, label: "Branch name" });
-          if (n) gitActions.createBranch(n, sha).then((ok) => { if (ok) gitActions.checkout(n); });
+          if (n && sameRepo()) gitActions.createBranch(n, sha).then((ok) => { if (ok) gitActions.checkout(n); });
         },
       },
     ];
diff --git a/src/lib/components/WorkingCopyView.svelte b/src/lib/components/WorkingCopyView.svelte
index 9ac6c0f..c76143a 100644
--- a/src/lib/components/WorkingCopyView.svelte
+++ b/src/lib/components/WorkingCopyView.svelte
@@ -8,7 +8,7 @@
   import CommitComposer from "./CommitComposer.svelte";
   import FileTree from "./FileTree.svelte";
   import { buildFileTree } from "../fileTree";
-  import { resolveSection, type WorkingSection } from "../workingSection";
+  import { renderedPresence, resolveSection, type WorkingSection } from "../workingSection";
   import type { WorkingFile } from "../types";
   import { crossfade, fade } from "svelte/transition";
   import { flip } from "svelte/animate";
@@ -62,15 +62,20 @@
 
   // Which RENDERED lists currently hold the selected path — sections are lists on screen,
   // not file states. A partially-staged file is in two of them at once, which is precisely
-  // why the clicked section has to be recorded. Note `unstagedDisplay`, not `unstagedFiles`:
-  // with unifyUnstaged on, untracked rows are rendered in the Unstaged list and report
-  // "unstaged", so presence has to agree or the selection resolves to a section that has
-  // no rows in that mode.
-  const presence = $derived({
-    staged: selectedFile !== null && stagedFiles.some((f) => f.path === selectedFile),
-    unstaged: selectedFile !== null && unstagedDisplay.some((f) => f.path === selectedFile),
-    untracked: selectedFile !== null && untrackedFiles.some((f) => f.path === selectedFile),
-  });
+  // why the clicked section has to be recorded. The merged-list handling lives in
+  // `renderedPresence` rather than here: computing the three fields inline is how they came
+  // to disagree about what "rendered" means.
+  const presence = $derived(
+    renderedPresence(
+      selectedFile,
+      {
+        staged: stagedFiles.map((f) => f.path),
+        unstaged: unstagedFiles.map((f) => f.path),
+        untracked: untrackedFiles.map((f) => f.path),
+      },
+      appState.unifyUnstaged,
+    ),
+  );
 
   // The section the pane actually shows: the one the user clicked, or — if the file has
   // since left it (they staged all of it, say) — wherever it went. See resolveSection().
@@ -87,8 +92,12 @@
   // Untracked files have no index entry, so the regular diff is empty — they need the
   // `git diff --no-index` path (and hunk/line staging doesn't apply to them). This is a
   // property of the FILE, not of the section: with unifyUnstaged on, an untracked file
-  // is rendered in the Unstaged list but still needs --no-index.
-  const selectedIsUntracked = $derived(presence.untracked);
+  // is rendered in the Unstaged list but still needs --no-index. Read from the file list,
+  // NOT from `presence.untracked`, which answers the narrower "is the Untracked section
+  // showing this row" and is false while merging.
+  const selectedIsUntracked = $derived(
+    selectedFile !== null && untrackedFiles.some((f) => f.path === selectedFile),
+  );
 
   // Whether the selected file is displayed in the Unstaged section — including an
   // untracked file that unifyUnstaged has merged into that list, which `presence.unstaged`
diff --git a/src/lib/workingSection.test.ts b/src/lib/workingSection.test.ts
index a8a75f5..f4a2275 100644
--- a/src/lib/workingSection.test.ts
+++ b/src/lib/workingSection.test.ts
@@ -1,5 +1,10 @@
 import { describe, it, expect } from "vitest";
-import { resolveSection, type SectionPresence, type WorkingSection } from "./workingSection";
+import {
+  renderedPresence,
+  resolveSection,
+  type SectionPresence,
+  type WorkingSection,
+} from "./workingSection";
 
 const present = (p: Partial<SectionPresence> = {}): SectionPresence => ({
   staged: false,
@@ -72,3 +77,38 @@ describe("resolveSection", () => {
     }
   });
 });
+
+describe("renderedPresence", () => {
+  const files = { staged: ["s.txt"], unstaged: ["u.txt"], untracked: ["n.txt"] };
+
+  it("reports nothing for no selection", () => {
+    expect(renderedPresence(null, files, false)).toEqual(present());
+  });
+
+  it("maps each file to its own section when the lists are separate", () => {
+    expect(renderedPresence("s.txt", files, false)).toEqual(present({ staged: true }));
+    expect(renderedPresence("u.txt", files, false)).toEqual(present({ unstaged: true }));
+    expect(renderedPresence("n.txt", files, false)).toEqual(present({ untracked: true }));
+  });
+
+  it("sees a partially-staged file in both lists at once", () => {
+    const both = { staged: ["p.txt"], unstaged: ["p.txt"], untracked: [] };
+    expect(renderedPresence("p.txt", both, false)).toEqual(present({ staged: true, unstaged: true }));
+  });
+
+  // The bug: with unifyUnstaged on there IS no Untracked list on screen — those rows are
+  // rendered in Unstaged and report "unstaged". Reporting untracked presence anyway let
+  // resolveSection keep a recorded "untracked" and resolve to a section with no rows, so
+  // nothing highlighted and the Unstaged header offered "Stage all" instead of "Stage".
+  it("moves untracked presence into Unstaged when the lists are merged", () => {
+    expect(renderedPresence("n.txt", files, true)).toEqual(present({ unstaged: true }));
+  });
+
+  it("resolves a recorded untracked selection to Unstaged once merging is enabled", () => {
+    const before = renderedPresence("n.txt", files, false);
+    expect(resolveSection("untracked", before)).toBe("untracked");
+
+    const after = renderedPresence("n.txt", files, true);
+    expect(resolveSection("untracked", after)).toBe("unstaged");
+  });
+});
diff --git a/src/lib/workingSection.ts b/src/lib/workingSection.ts
index 01c009f..142af37 100644
--- a/src/lib/workingSection.ts
+++ b/src/lib/workingSection.ts
@@ -27,6 +27,38 @@ export interface SectionPresence {
   untracked: boolean;
 }
 
+/**
+ * Build a `SectionPresence` from the working-copy file lists.
+ *
+ * The rule above — presence describes lists ON SCREEN, not file states — is easy to state and
+ * easy to get wrong: it has been violated once per field. Deriving it inline in the component
+ * meant `unstaged` was computed from the merged display list while `untracked` was computed
+ * from the raw file state, so with merging on a path reported presence in BOTH, `resolveSection`
+ * kept the recorded `"untracked"`, and the pane resolved to a section with no rows — nothing
+ * highlighted and the Unstaged header offered "Stage all" instead of "Stage". Encoding it here
+ * keeps the two fields from drifting apart again, and makes the merged case testable.
+ *
+ * `untracked` is asked twice for different reasons; do not conflate them. This answers "is the
+ * Untracked SECTION showing this row", which is false while merging. Whether the FILE is
+ * untracked — which decides `git diff --no-index` and disables hunk staging — is a separate
+ * question the caller must answer from the file list regardless of mode.
+ */
+export function renderedPresence(
+  path: string | null,
+  files: { staged: string[]; unstaged: string[]; untracked: string[] },
+  unifyUnstaged: boolean,
+): SectionPresence {
+  if (path === null) return { staged: false, unstaged: false, untracked: false };
+  const holds = (list: string[]) => list.includes(path);
+  return {
+    staged: holds(files.staged),
+    // With merging on, the Unstaged list renders the untracked rows too.
+    unstaged: holds(files.unstaged) || (unifyUnstaged && holds(files.untracked)),
+    // ...and the Untracked section is not rendered at all.
+    untracked: !unifyUnstaged && holds(files.untracked),
+  };
+}
+
 /**
  * The section the diff pane should actually show for the selected file.
  *