diff --git a/package-lock.json b/package-lock.json
index d62b89a..976717a 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "json-diff-ts",
-  "version": "5.0.0-alpha.8",
+  "version": "5.0.0-alpha.9",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "json-diff-ts",
-      "version": "5.0.0-alpha.8",
+      "version": "5.0.0-alpha.9",
       "license": "MIT",
       "devDependencies": {
         "@eslint/js": "^10.0.1",
diff --git a/package.json b/package.json
index 75f856a..8e63118 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "json-diff-ts",
-  "version": "5.0.0-alpha.8",
+  "version": "5.0.0-alpha.9",
   "description": "Modern TypeScript JSON diff library - Zero dependencies, high performance, ESM + CommonJS support. Calculate and apply differences between JSON objects with advanced features like key-based array diffing, JSONPath support, and atomic changesets.",
   "main": "./dist/index.cjs",
   "module": "./dist/index.js",
diff --git a/src/jsonAtom.ts b/src/jsonAtom.ts
index f33a8b2..92fd948 100644
--- a/src/jsonAtom.ts
+++ b/src/jsonAtom.ts
@@ -213,7 +213,8 @@ function walkChanges(
 
       if (change.embeddedKey) {
         // Array level — process each child with filter expression
-        for (const childChange of change.changes) {
+        const orderedChildChanges = orderArrayChildChanges(change.changes, change.embeddedKey);
+        for (const childChange of orderedChildChanges) {
           const filterPath = buildCanonicalFilterPath(
             childPath,
             change.embeddedKey,
@@ -245,6 +246,66 @@ function walkChanges(
   }
 }
 
+function orderArrayChildChanges(changes: IChange[], embeddedKey: string | FunctionKey): IChange[] {
+  if (embeddedKey !== '$index') {
+    return changes;
+  }
+
+  type OrderedGroup = { kind: 'pure-remove' } | { kind: 'preserved'; changes: IChange[] };
+  const groups: OrderedGroup[] = [];
+  const pureRemoves: IChange[] = [];
+
+  for (let i = 0; i < changes.length; i++) {
+    const current = changes[i];
+    const next = changes[i + 1];
+
+    // Keep REMOVE+ADD type-change pairs together and in original order.
+    if (
+      current.type === Operation.REMOVE &&
+      next &&
+      next.type === Operation.ADD &&
+      String(current.key) === String(next.key)
+    ) {
+      groups.push({ kind: 'preserved', changes: [current, next] });
+      i++;
+      continue;
+    }
+
+    if (current.type === Operation.REMOVE) {
+      pureRemoves.push(current);
+      groups.push({ kind: 'pure-remove' });
+      continue;
+    }
+
+    groups.push({ kind: 'preserved', changes: [current] });
+  }
+
+  if (pureRemoves.length < 2) {
+    return changes;
+  }
+
+  const removeIndices = pureRemoves.map((change) => Number(change.key));
+  /* istanbul ignore next -- $index keys are always integer-like from diff(); fallback is defensive */
+  if (removeIndices.some((idx) => !Number.isInteger(idx))) {
+    // Defensive fallback: if keys are not numeric, keep original order.
+    return changes;
+  }
+
+  pureRemoves.sort((a, b) => Number(b.key) - Number(a.key));
+
+  const ordered: IChange[] = [];
+  let removeIndex = 0;
+  for (const group of groups) {
+    if (group.kind === 'pure-remove') {
+      ordered.push(pureRemoves[removeIndex++]);
+    } else {
+      ordered.push(...group.changes);
+    }
+  }
+
+  return ordered;
+}
+
 function emitLeafOp(
   change: IChange,
   path: string,
diff --git a/tests/jsonAtom.test.ts b/tests/jsonAtom.test.ts
index 5c8d59f..cd52cfb 100644
--- a/tests/jsonAtom.test.ts
+++ b/tests/jsonAtom.test.ts
@@ -203,6 +203,112 @@ describe('diffAtom', () => {
     });
   });
 
+  it('applies multiple index-based removes correctly without identity keys (#404)', () => {
+    const oldObj = {
+      bankAccounts: [
+        { iban: 'DE12345678901234567890', bic: 'BIC123456' },
+        { iban: 'DE23456789012345678901', bic: 'BIC234567' },
+        { iban: 'DE23456789012345678902', bic: 'BIC234567' },
+      ],
+    };
+    const newObj = {
+      bankAccounts: [{ iban: 'DE11456789012345678999', bic: 'BIC123456' }],
+    };
+
+    const atom = diffAtom(oldObj, newObj);
+    expect(atom.operations).toEqual([
+      {
+        op: 'replace',
+        path: '$.bankAccounts[0].iban',
+        oldValue: 'DE12345678901234567890',
+        value: 'DE11456789012345678999',
+      },
+      {
+        op: 'remove',
+        path: '$.bankAccounts[2]',
+        oldValue: { iban: 'DE23456789012345678902', bic: 'BIC234567' },
+      },
+      {
+        op: 'remove',
+        path: '$.bankAccounts[1]',
+        oldValue: { iban: 'DE23456789012345678901', bic: 'BIC234567' },
+      },
+    ]);
+
+    const applied = applyAtom(structuredClone(oldObj), atom);
+    expect(applied).toEqual(newObj);
+  });
+
+  it('emits index-based remove operations in descending order for nested arrays', () => {
+    const oldObj = { items: [1, 2, 3, 4] };
+    const newObj = { items: [1] };
+
+    const atom = diffAtom(oldObj, newObj);
+    const removeIndices = atom.operations
+      .filter((op) => op.op === 'remove')
+      .map((op) => Number(op.path.match(/\[(\d+)\]$/)?.[1]));
+
+    expect(removeIndices.length).toBeGreaterThanOrEqual(2);
+    expect(removeIndices).toEqual([...removeIndices].sort((a, b) => b - a));
+
+    const applied = applyAtom(structuredClone(oldObj), atom);
+    expect(applied).toEqual(newObj);
+  });
+
+  it('keeps non-remove operations while sorting multiple index removes descending', () => {
+    const oldObj = { items: ['a', 'b', 'c', 'd'] };
+    const newObj = { items: ['z', 'b'] };
+
+    const atom = diffAtom(oldObj, newObj);
+    const removeIndices = atom.operations
+      .filter((op) => op.op === 'remove')
+      .map((op) => Number(op.path.match(/\[(\d+)\]$/)?.[1]));
+
+    expect(atom.operations.some((op) => op.op === 'replace')).toBe(true);
+    expect(removeIndices.length).toBeGreaterThanOrEqual(2);
+    expect(removeIndices).toEqual([...removeIndices].sort((a, b) => b - a));
+
+    const applied = applyAtom(structuredClone(oldObj), atom);
+    expect(applied).toEqual(newObj);
+  });
+
+  it('keeps index type-change REMOVE+ADD pairs in order while still applying correctly', () => {
+    const oldObj = { items: [1, 2, 3, 4] };
+    const newObj = { items: ['x', 2] };
+
+    const atom = diffAtom(oldObj, newObj);
+    expect(applyAtom(structuredClone(oldObj), atom)).toEqual(newObj);
+
+    // Ensure pure removes (excluding paired type-change REMOVE+ADD at same index) stay descending.
+    const addIndices = new Set(
+      atom.operations
+        .filter((op) => op.op === 'add')
+        .map((op) => Number(op.path.match(/\[(\d+)\]$/)?.[1]))
+    );
+    const pureRemoveIndices = atom.operations
+      .filter((op) => op.op === 'remove')
+      .map((op) => Number(op.path.match(/\[(\d+)\]$/)?.[1]))
+      .filter((idx) => !addIndices.has(idx));
+
+    expect(pureRemoveIndices).toEqual([...pureRemoveIndices].sort((a, b) => b - a));
+  });
+
+  it('preserves same-index REMOVE+ADD pairs for pure index type changes (P1 badge case)', () => {
+    const oldObj = { a: [1, 2] };
+    const newObj = { a: [[1], [2]] };
+
+    const atom = diffAtom(oldObj, newObj);
+    const applied = applyAtom(structuredClone(oldObj), atom);
+
+    expect(applied).toEqual(newObj);
+    expect(atom.operations).toEqual([
+      { op: 'remove', path: '$.a[0]', oldValue: 1 },
+      { op: 'add', path: '$.a[0]', value: [1] },
+      { op: 'remove', path: '$.a[1]', oldValue: 2 },
+      { op: 'add', path: '$.a[1]', value: [2] },
+    ]);
+  });
+
   it('handles arrays with named key (string IDs)', () => {
     const atom = diffAtom(
       { items: [{ id: '1', name: 'Widget' }] },