diff --git a/bun.lock b/bun.lock
index 82d4740ea..71b65b73c 100644
--- a/bun.lock
+++ b/bun.lock
@@ -735,7 +735,7 @@
 
     "isexe": ["isexe@3.1.5", "", {}, "sha512-6B3tLtFqtQS4ekarvLVMZ+X+VlvQekbe4taUkf/rhVO3d/h0M2rfARm/pXLcPEsjjMsFgrFgSrhQIxcSVrBz8w=="],
 
-    "isomorphic-git": ["isomorphic-git@1.41.9", "", { "dependencies": { "async-lock": "^1.4.1", "clean-git-ref": "^2.0.1", "crc-32": "^1.2.0", "diff3": "0.0.3", "ignore": "^5.1.4", "minimisted": "^2.0.0", "pako": "^1.0.10", "pify": "^4.0.1", "readable-stream": "^4.0.0", "sha.js": "^2.4.12", "simple-get": "^4.0.1" }, "bin": { "isogit": "cli.cjs" } }, "sha512-WOh4ujm5mznHphzQvwj9bVj+pQpV0oZ8H4lAnh4dSaie+lN/lJ2rb6rNOOcP+2m4z8IOQp186TkEULD28NMBJg=="],
+    "isomorphic-git": ["isomorphic-git@1.44.2", "", { "dependencies": { "async-lock": "^1.4.1", "clean-git-ref": "^2.0.1", "crc-32": "^1.2.0", "diff3": "0.0.3", "ignore": "^5.1.4", "minimisted": "^2.0.0", "pako": "^1.0.10", "pify": "^4.0.1", "readable-stream": "^4.0.0", "sha.js": "^2.4.12", "simple-get": "^4.0.1" }, "bin": { "isogit": "cli.cjs" } }, "sha512-RORfhiNxaHRkGXvTiIW1SU6ngH/jW7UnKndvIToGxrGja7s317CUcZ5chENyinnyCPz7Z4vAefA75Ty1Zsyc8w=="],
 
     "isomorphic-textencoder": ["isomorphic-textencoder@1.0.1", "", { "dependencies": { "fast-text-encoding": "^1.0.0" } }, "sha512-676hESgHullDdHDsj469hr+7t3i/neBKU9J7q1T4RHaWwLAsaQnywC0D1dIUId0YZ+JtVrShzuBk1soo0+GVcQ=="],
 
diff --git a/src/session/optimized-context-store.test.ts b/src/session/optimized-context-store.test.ts
index c6bfd9835..c66ac13c0 100644
--- a/src/session/optimized-context-store.test.ts
+++ b/src/session/optimized-context-store.test.ts
@@ -1,4 +1,5 @@
 import { defined } from "../../testkit/defined.js";
+import { withMockedModuleDuring } from "../../testkit/mock-module.js";
 import { describe, test, expect } from "bun:test";
 import fs from "node:fs";
 import os from "node:os";
@@ -1726,4 +1727,50 @@ describe("createOptimizedContextStore prompt dedupe (CL-9026)", () => {
     expect(tree).not.toContain(extraPrompt);
     expect(turnTexts((await store.load()).turns)).toEqual(turnTexts(live));
   });
+
+  test("one remove failure still unstages the other paths in one index write", async () => {
+    const dir = tempDir();
+    const store = await createOptimizedContextStore(dir);
+    const huge = "x".repeat(300_000);
+    const live = [turn(`live-${huge}`), turn("live-tail")];
+    await store.writeTurns([...live]);
+    await store.writePrompt([turn(`prompt-${huge}`), turn("prompt-tail")]);
+    await store.writeMetadata(EMPTY_CHECKPOINT_METADATA);
+    await store.commit({ message: "two prompt segments" });
+    const extraPrompt = segmentFileName(PROMPT_FILE, 1);
+    expect(await gitLsTree(dir)).toEqual(
+      expect.arrayContaining([PROMPT_FILE, extraPrompt]),
+    );
+
+    await store.writePrompt(cloneTurns(live));
+    await store.writeMetadata(EMPTY_CHECKPOINT_METADATA);
+
+    const removeCalls: (string | string[])[] = [];
+    await withMockedModuleDuring(
+      import.meta.resolve("isomorphic-git"),
+      (real: typeof import("isomorphic-git")) => {
+        const remove: typeof real.default.remove = async (args) => {
+          removeCalls.push(args.filepath);
+          const paths = Array.isArray(args.filepath)
+            ? args.filepath
+            : [args.filepath];
+          if (paths.includes(extraPrompt)) {
+            throw new Error("index write failed");
+          }
+          return real.default.remove(args);
+        };
+        return { ...real, default: { ...real.default, remove } };
+      },
+      () => store.commit({ message: "drop prompt segments" }),
+    );
+
+    const tree = await gitLsTree(dir);
+    expect(tree).not.toContain(PROMPT_FILE);
+    expect(tree).toContain(extraPrompt);
+    const written = removeCalls.filter((filepath) => {
+      const paths = Array.isArray(filepath) ? filepath : [filepath];
+      return !paths.includes(extraPrompt);
+    });
+    expect(written).toEqual([[PROMPT_FILE]]);
+  });
 });
diff --git a/src/session/optimized-context-store.ts b/src/session/optimized-context-store.ts
index 5558ca5ea..157b5ae69 100644
--- a/src/session/optimized-context-store.ts
+++ b/src/session/optimized-context-store.ts
@@ -1332,14 +1332,34 @@ export async function createSessionStores(
           const remove = [...new Set(toRemove)].filter((p) => !add.includes(p));
           extraPaths = [...new Set([...add, ...remove])];
 
-          for (const filepath of add) {
-            await git.add({ fs, dir, filepath });
+          // Array `git.add` / `git.remove` each write the index once.
+          // Array `remove` is isomorphic-git 1.43.0; array `add` is older.
+          // A mid-batch add failure leaves the index unwritten. Only the
+          // outer catch calls `resetIndexPaths`.
+          if (add.length > 0) {
+            await git.add({ fs, dir, filepath: add });
           }
-          for (const filepath of remove) {
+          if (remove.length > 0) {
             try {
-              await git.remove({ fs, dir, filepath });
-            } catch {
-              // Already absent from the index.
+              await git.remove({ fs, dir, filepath: remove });
+            } catch (cause) {
+              // `GitIndex.delete` does not throw when a path is absent, so
+              // this is an index lock or write. It aborts before the index
+              // write. Skip the failing path and write the rest once.
+              let unstaged = false;
+              if (remove.length > 1) {
+                for (let index = 0; index < remove.length; index++) {
+                  const rest = remove.filter((_, other) => other !== index);
+                  try {
+                    await git.remove({ fs, dir, filepath: rest });
+                    unstaged = true;
+                    break;
+                  } catch {
+                    // This omission still aborted before the index write.
+                  }
+                }
+              }
+              if (!unstaged) throw cause;
             }
           }
           const committed = await base.commit(options, signal);