diff --git a/packages/react-native/scripts/__tests__/replace-rncore-version-test.js b/packages/react-native/scripts/__tests__/replace-rncore-version-test.js
index f435e2fa1a9..ad077aa93dd 100644
--- a/packages/react-native/scripts/__tests__/replace-rncore-version-test.js
+++ b/packages/react-native/scripts/__tests__/replace-rncore-version-test.js
@@ -19,6 +19,18 @@ const path = require('node:path');
 const VERSION = '0.87.0-test';
 const SLICE = 'ios-arm64_x86_64-simulator';
 const BINARY = path.join(SLICE, 'React.framework', 'React');
+const SCRIPT = require.resolve('../replace-rncore-version.js');
+const MARKER = path.join('React-Core-prebuilt', '.last_build_configuration');
+
+// Runs the script the way the "[RNCore] Replace React Native Core for the right
+// configuration" build phase does, from Pods/ and through the CLI entry point.
+function runScriptPhase(podsRoot, configuration) {
+  return execFileSync(
+    process.execPath,
+    [SCRIPT, '-c', configuration, '-r', VERSION, '-p', podsRoot],
+    {cwd: podsRoot, encoding: 'utf8'},
+  );
+}
 
 function writeFile(filePath, contents) {
   fs.mkdirSync(path.dirname(filePath), {recursive: true});
@@ -119,6 +131,73 @@ describe('replaceRNCoreConfiguration', () => {
     expect(fs.readFileSync(expoModuleMap, 'utf8')).toBe('module React {}\n');
   });
 
+  // Regression tests for #57598. The marker used to be written only after the
+  // framework had already been replaced, so a build cancelled in between left it
+  // naming a flavor that was no longer on disk. Every later build for that
+  // flavor then took the "nothing to do" path and linked against the other
+  // configuration's core, which fails with undefined C++ symbols and which a
+  // clean does not undo because the pod directory survives it.
+  describe('marker bookkeeping', () => {
+    const marker = () => path.join(podsRoot, MARKER);
+    const binary = () =>
+      fs.readFileSync(path.join(pod, 'React.xcframework', BINARY), 'utf8');
+
+    it('records the configuration when it skips a fresh install', () => {
+      // `pod install` leaves the debug flavor and no marker, so a Debug build
+      // has nothing to swap. It still has to write down what is on disk,
+      // otherwise the state stays implicit and stays unverifiable.
+      expect(fs.existsSync(marker())).toBe(false);
+
+      runScriptPhase(podsRoot, 'Debug');
+
+      expect(fs.readFileSync(marker(), 'utf8')).toBe('Debug');
+      expect(binary()).toBe('binary-Debug');
+    });
+
+    it('invalidates the marker before it touches the framework', () => {
+      fs.writeFileSync(marker(), 'Debug');
+      // Drop the tarball so the Release run fails once it is already under way,
+      // standing in for a build cancelled part way through the swap.
+      fs.rmSync(
+        path.join(
+          podsRoot,
+          'ReactNativeCore-artifacts',
+          `reactnative-core-${VERSION.toLowerCase()}-release.tar.gz`,
+        ),
+      );
+
+      expect(() => runScriptPhase(podsRoot, 'Release')).toThrow();
+
+      // The marker must no longer claim Debug: the framework may already have
+      // been swapped, and a Debug build that trusts it would silently skip.
+      expect(fs.readFileSync(marker(), 'utf8')).not.toBe('Debug');
+    });
+
+    it('replaces the framework when the marker shows an unfinished swap', () => {
+      buildTarball(podsRoot, 'Debug');
+      // A swap that was interrupted: the Release flavor is on disk and the
+      // marker never got its final value.
+      replaceRNCoreConfiguration('Release', VERSION, podsRoot);
+      fs.writeFileSync(marker(), 'in-progress');
+      expect(binary()).toBe('binary-Release');
+
+      runScriptPhase(podsRoot, 'Debug');
+
+      expect(binary()).toBe('binary-Debug');
+      expect(fs.readFileSync(marker(), 'utf8')).toBe('Debug');
+    });
+
+    it('still skips when the marker already matches the configuration', () => {
+      fs.writeFileSync(marker(), 'Release');
+      const before = binary();
+
+      const output = runScriptPhase(podsRoot, 'Release');
+
+      expect(output).toContain('No need to replace React-Core-prebuilt');
+      expect(binary()).toBe(before);
+    });
+  });
+
   it('fails when the tarball has no React.xcframework', () => {
     const stage = fs.mkdtempSync(path.join(podsRoot, 'stage-bad-'));
     writeFile(path.join(stage, 'unrelated.txt'), 'nope');
diff --git a/packages/react-native/scripts/replace-rncore-version.js b/packages/react-native/scripts/replace-rncore-version.js
index dbfc11ecaa4..07e4edba740 100644
--- a/packages/react-native/scripts/replace-rncore-version.js
+++ b/packages/react-native/scripts/replace-rncore-version.js
@@ -18,6 +18,11 @@ const yargs = require('yargs');
 
 const LAST_BUILD_FILENAME = 'React-Core-prebuilt/.last_build_configuration';
 
+// Stored in LAST_BUILD_FILENAME while the framework on disk is being swapped.
+// It is not a valid configuration, so a run that finds it knows the previous
+// swap did not finish and the flavor on disk cannot be trusted.
+const REPLACEMENT_IN_PROGRESS = 'in-progress';
+
 function validateBuildConfiguration(configuration /*: string */) {
   if (!['Debug', 'Release'].includes(configuration)) {
     throw new Error(`Invalid configuration ${configuration}`);
@@ -42,13 +47,24 @@ function shouldReplaceRnCoreConfiguration(configuration /*: string */) {
       );
       return false;
     }
+    // Anything else, including REPLACEMENT_IN_PROGRESS left by a swap that was
+    // cancelled or killed, means the flavor on disk is not the requested one or
+    // is unknown. Replace it.
+    return true;
   }
 
-  // Assumption: if there is no stored last build, we assume that it was build for debug.
-  if (!fileExists && configuration === 'Debug') {
+  // No marker means `pod install` has just laid the pod down and nothing has
+  // swapped it since, because a swap records REPLACEMENT_IN_PROGRESS before it
+  // touches the framework. The podspec source is always the debug tarball (see
+  // resolve_podspec_source in scripts/cocoapods/rncore.rb), so the flavor on
+  // disk is Debug and a Debug build has nothing to do.
+  if (configuration === 'Debug') {
     console.log(
       'No previous build detected, but Debug Configuration. No need to replace React-Core-prebuilt',
     );
+    // Record the assumption rather than leaving it implicit, so the state is
+    // readable and a later run never has to make it again.
+    updateLastBuildConfiguration(configuration);
     return false;
   }
 
@@ -130,6 +146,10 @@ function updateLastBuildConfiguration(configuration /*: string */) {
   fs.writeFileSync(LAST_BUILD_FILENAME, configuration);
 }
 
+function markReplacementInProgress() /*: void */ {
+  fs.writeFileSync(LAST_BUILD_FILENAME, REPLACEMENT_IN_PROGRESS);
+}
+
 function main(
   configuration /*: string */,
   version /*: string */,
@@ -142,6 +162,12 @@ function main(
     return;
   }
 
+  // Invalidate the marker before the framework is touched. A build cancelled
+  // between the swap and the update used to leave the marker naming a flavor
+  // that was no longer on disk, and every later build for that flavor then took
+  // the skip path and linked against the wrong core, which a clean does not
+  // undo. Recording the swap first makes an interrupted run recoverable.
+  markReplacementInProgress();
   replaceRNCoreConfiguration(configuration, version, podsRoot);
   updateLastBuildConfiguration(configuration);
   console.log('Done replacing React Native prebuilt');