diff --git a/cli/src/__tests__/worktree.test.ts b/cli/src/__tests__/worktree.test.ts
index ba8d3339c3..b4834dd512 100644
--- a/cli/src/__tests__/worktree.test.ts
+++ b/cli/src/__tests__/worktree.test.ts
@@ -488,14 +488,34 @@ describe("worktree helpers", () => {
     expect(full.nullifyColumns).toEqual({});
   });
 
-  it("rejects a source migration journal that is ahead of the code journal", () => {
+  it("rejects a source migration journal that diverges from the code journal", () => {
     expect(() => resolveWorktreeSeedMigrationRevision({
       status: "upToDate",
       tableCount: 1,
       availableMigrations: ["0001_initial.sql", "0002_current.sql"],
-      appliedMigrations: ["0001_initial.sql", "0002_current.sql"],
+      appliedMigrations: ["0001_initial.sql", "0003_unknown.sql"],
       journalEntryCount: 3,
-    }, "sourcePrefix")).toThrow("Migration journal is ahead of this Paperclip checkout");
+    }, "sourcePrefix")).toThrow("Migration journal is not a prefix of this Paperclip checkout");
+  });
+
+  it("accepts a current source whose migration application order differs from filename order", () => {
+    expect(resolveWorktreeSeedMigrationRevision({
+      status: "upToDate",
+      tableCount: 1,
+      availableMigrations: [
+        "0001_initial.sql",
+        "0002_renumbered.sql",
+        "0003_applied_earlier.sql",
+        "0004_current.sql",
+      ],
+      appliedMigrations: [
+        "0001_initial.sql",
+        "0003_applied_earlier.sql",
+        "0002_renumbered.sql",
+        "0004_current.sql",
+      ],
+      journalEntryCount: 6,
+    }, "upToDate")).toBe("0004_current.sql");
   });
 
   it("accepts a source migration journal that is multiple revisions behind", () => {
@@ -508,9 +528,9 @@ describe("worktree helpers", () => {
         "0003_pending.sql",
         "0004_pending.sql",
       ],
-      appliedMigrations: ["0001_initial.sql", "0002_applied.sql"],
+      appliedMigrations: ["0002_applied.sql", "0001_initial.sql"],
       pendingMigrations: ["0003_pending.sql", "0004_pending.sql"],
-      journalEntryCount: 2,
+      journalEntryCount: 3,
       reason: "pending-migrations",
     }, "sourcePrefix")).toBe("0002_applied.sql");
   });
@@ -1244,7 +1264,7 @@ describe("worktree helpers", () => {
   });
 
   itEmbeddedPostgres(
-    "seeds a source whose migration journal is behind the code journal",
+    "seeds a lagging source whose migration application order differs from filename order",
     async () => {
       const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-auth-seed-"));
       const worktreeRoot = path.join(tempRoot, "PAP-999-auth-seed");
@@ -1264,7 +1284,30 @@ describe("worktree helpers", () => {
           DELETE FROM "drizzle"."__drizzle_migrations"
           WHERE "id" = (
             SELECT max("id") FROM "drizzle"."__drizzle_migrations"
+          );
+
+          WITH pair AS (
+            SELECT
+              array_agg("id" ORDER BY "id" DESC) AS ids,
+              array_agg("hash" ORDER BY "id" DESC) AS hashes
+            FROM (
+              SELECT "id", "hash"
+              FROM "drizzle"."__drizzle_migrations"
+              ORDER BY "id" DESC
+              LIMIT 2
+            ) latest
           )
+          UPDATE "drizzle"."__drizzle_migrations" migrations
+          SET "hash" = CASE
+            WHEN migrations."id" = pair.ids[1] THEN pair.hashes[2]
+            WHEN migrations."id" = pair.ids[2] THEN pair.hashes[1]
+            ELSE migrations."hash"
+          END
+          FROM pair
+          WHERE migrations."id" IN (pair.ids[1], pair.ids[2]);
+
+          INSERT INTO "drizzle"."__drizzle_migrations" ("hash", "created_at")
+          VALUES ('stale-unresolvable-migration-hash', 0)
         `);
         await sourceDbClient.$client.end({ timeout: 5 });
         const laggingMigrationState = await inspectMigrations(sourceDb.connectionString);
@@ -1273,7 +1316,18 @@ describe("worktree helpers", () => {
           throw new Error("Expected the source migration journal to lag the code journal");
         }
         expect(laggingMigrationState.pendingMigrations).toHaveLength(1);
-        const sourceMigrationRevision = laggingMigrationState.appliedMigrations.at(-1);
+        const expectedAppliedPrefix = laggingMigrationState.availableMigrations.slice(
+          0,
+          laggingMigrationState.appliedMigrations.length,
+        );
+        expect(laggingMigrationState.appliedMigrations).not.toEqual(expectedAppliedPrefix);
+        expect([...laggingMigrationState.appliedMigrations].sort()).toEqual(
+          [...expectedAppliedPrefix].sort(),
+        );
+        expect(laggingMigrationState.journalEntryCount).toBeGreaterThan(
+          laggingMigrationState.appliedMigrations.length,
+        );
+        const sourceMigrationRevision = expectedAppliedPrefix.at(-1);
         expect(sourceMigrationRevision).toBeTruthy();
 
         fs.mkdirSync(path.dirname(sourceKeyPath), { recursive: true });
diff --git a/cli/src/commands/worktree.ts b/cli/src/commands/worktree.ts
index be6926c220..d31dabaefc 100644
--- a/cli/src/commands/worktree.ts
+++ b/cli/src/commands/worktree.ts
@@ -1416,20 +1416,14 @@ export function resolveWorktreeSeedMigrationRevision(
   migrationState: Awaited<ReturnType<typeof inspectMigrations>>,
   requirement: "sourcePrefix" | "upToDate",
 ): string {
-  if (migrationState.journalEntryCount > migrationState.availableMigrations.length) {
-    throw new Error(
-      `Migration journal is ahead of this Paperclip checkout (${migrationState.journalEntryCount} applied migration(s), ${migrationState.availableMigrations.length} available).`,
-    );
-  }
-
   const expectedAppliedPrefix = migrationState.availableMigrations.slice(
     0,
     migrationState.appliedMigrations.length,
   );
+  const appliedMigrationNames = new Set(migrationState.appliedMigrations);
   if (
-    migrationState.appliedMigrations.some(
-      (migration, index) => migration !== expectedAppliedPrefix[index],
-    )
+    appliedMigrationNames.size !== expectedAppliedPrefix.length ||
+    expectedAppliedPrefix.some((migration) => !appliedMigrationNames.has(migration))
   ) {
     throw new Error("Migration journal is not a prefix of this Paperclip checkout's migration journal.");
   }
@@ -1440,7 +1434,7 @@ export function resolveWorktreeSeedMigrationRevision(
     );
   }
 
-  const migrationRevision = migrationState.appliedMigrations.at(-1);
+  const migrationRevision = expectedAppliedPrefix.at(-1);
   if (!migrationRevision) {
     throw new Error("Migration journal has no applied revision.");
   }