diff --git a/src/Caching/Detector/ChangedFilesDetector.php b/src/Caching/Detector/ChangedFilesDetector.php
index 173cfabc055..5ff2fee21c6 100644
--- a/src/Caching/Detector/ChangedFilesDetector.php
+++ b/src/Caching/Detector/ChangedFilesDetector.php
@@ -26,6 +26,13 @@ final class ChangedFilesDetector
     // scopes the per-file cache key to the active --only / --only-suffix / --filter selection (empty = full run)
     private string $scopeSuffix = '';
 
+    private ?string $configurationCacheKey = null;
+
+    /**
+     * @var array{hash: string, rules: string[], sets: string[], skip: string[]}|null
+     */
+    private ?array $configurationSnapshot = null;
+
     public function __construct(
         private readonly FileHashComputer $fileHashComputer,
         private readonly Cache $cache,
@@ -95,6 +102,15 @@ public function invalidateFile(string $filePath): void
     public function clear(): void
     {
         $this->cache->clear();
+
+        // keep the snapshot of the current run, so the next run can still detect a configuration change
+        if ($this->configurationCacheKey !== null && $this->configurationSnapshot !== null) {
+            $this->cache->save(
+                $this->configurationCacheKey,
+                CacheKey::CONFIGURATION_HASH_KEY,
+                $this->configurationSnapshot
+            );
+        }
     }
 
     public function setFirstResolvedConfigFileInfo(string $filePath): void
@@ -141,7 +157,12 @@ private function createConfigurationSnapshot(string $filePath): array
     private function storeConfigurationDataHash(string $filePath, array $configurationSnapshot): void
     {
         $key = CacheKey::CONFIGURATION_HASH_KEY . '_' . $this->getFilePathCacheKey($filePath);
-        $this->invalidateCacheIfConfigurationChanged($key, $configurationSnapshot);
+        $oldCachedValue = $this->cache->load($key, CacheKey::CONFIGURATION_HASH_KEY);
+
+        $this->configurationCacheKey = $key;
+        $this->configurationSnapshot = $configurationSnapshot;
+
+        $this->invalidateCacheIfConfigurationChanged($oldCachedValue, $configurationSnapshot);
 
         $this->cache->save($key, CacheKey::CONFIGURATION_HASH_KEY, $configurationSnapshot);
     }
@@ -149,10 +170,8 @@ private function storeConfigurationDataHash(string $filePath, array $configurati
     /**
      * @param array{hash: string, rules: string[], sets: string[], skip: string[]} $configurationSnapshot
      */
-    private function invalidateCacheIfConfigurationChanged(string $key, array $configurationSnapshot): void
+    private function invalidateCacheIfConfigurationChanged(mixed $oldCachedValue, array $configurationSnapshot): void
     {
-        $oldCachedValue = $this->cache->load($key, CacheKey::CONFIGURATION_HASH_KEY);
-
         // first run, nothing to compare against
         if ($oldCachedValue === null) {
             return;
diff --git a/tests/Caching/Detector/ChangedFilesDetectorTest.php b/tests/Caching/Detector/ChangedFilesDetectorTest.php
index a904f939c04..2d2f49160fc 100644
--- a/tests/Caching/Detector/ChangedFilesDetectorTest.php
+++ b/tests/Caching/Detector/ChangedFilesDetectorTest.php
@@ -137,6 +137,26 @@ public function testCacheClearedWhenSkipRemoved(): void
         $this->assertTrue($this->changedFilesDetector->hasFileChanged($filePath));
     }
 
+    public function testCacheClearedWhenSkipRemovedAfterClearCacheRun(): void
+    {
+        SimpleParameterProvider::setParameter(Option::SKIP, ['Rector\\RuleA']);
+        $this->applyRules(['Rector\\RuleA', 'Rector\\RuleB']);
+
+        // --clear-cache wipes the cache after the configuration snapshot was stored
+        $this->changedFilesDetector->clear();
+
+        $filePath = __DIR__ . '/Source/file.php';
+        $this->changedFilesDetector->addCacheableFile($filePath);
+        $this->changedFilesDetector->cacheFile($filePath);
+        $this->assertFalse($this->changedFilesDetector->hasFileChanged($filePath));
+
+        // the next run removes the skip, the snapshot of the cleared run must still be there to compare
+        SimpleParameterProvider::setParameter(Option::SKIP, []);
+        $this->snapshotConfiguration();
+
+        $this->assertTrue($this->changedFilesDetector->hasFileChanged($filePath));
+    }
+
     public function testCacheClearedWhenOutputAffectingParameterChanged(): void
     {
         SimpleParameterProvider::setParameter(Option::FILE_EXTENSIONS, ['php']);