diff --git a/src/Configurator/CopyFromRecipeConfigurator.php b/src/Configurator/CopyFromRecipeConfigurator.php
index 0e18096b..6acf6377 100644
--- a/src/Configurator/CopyFromRecipeConfigurator.php
+++ b/src/Configurator/CopyFromRecipeConfigurator.php
@@ -31,7 +31,13 @@ public function configure(Recipe $recipe, $config, Lock $lock, array $options =
     public function unconfigure(Recipe $recipe, $config, Lock $lock)
     {
         $this->write('Removing files from recipe');
-        $this->removeFiles($config, $this->getRemovableFilesFromRecipeAndLock($recipe, $lock), $this->options->get('root-dir'));
+        $rootDir = $this->options->get('root-dir');
+
+        foreach ($this->options->getRemovableFiles($recipe, $lock) as $file) {
+            if ('.git' !== $file) { // never remove the main Git directory, even if it was created by a recipe
+                $this->removeFile($this->path->concatenate([$rootDir, $file]));
+            }
+        }
     }
 
     public function update(RecipeUpdate $recipeUpdate, array $originalConfig, array $newConfig): void
@@ -66,32 +72,6 @@ private function resolveTargetFolder(string $path, array $config): string
         return $path;
     }
 
-    private function getRemovableFilesFromRecipeAndLock(Recipe $recipe, Lock $lock): array
-    {
-        $lockedFiles = array_unique(
-            array_reduce(
-                array_column($lock->all(), 'files'),
-                function (array $carry, array $package) {
-                    return array_merge($carry, $package);
-                },
-                []
-            )
-        );
-
-        $removableFiles = $recipe->getFiles();
-
-        $lockedFiles = array_map('realpath', $lockedFiles);
-
-        // Compare file paths by their real path to abstract OS differences
-        foreach (array_keys($removableFiles) as $file) {
-            if (\in_array(realpath($file), $lockedFiles)) {
-                unset($removableFiles[$file]);
-            }
-        }
-
-        return $removableFiles;
-    }
-
     private function copyFiles(array $manifest, array $files, array $options): array
     {
         $copiedFiles = [];
@@ -148,28 +128,6 @@ private function copyFile(string $to, string $contents, bool $executable, array
         return $copiedFile;
     }
 
-    private function removeFiles(array $manifest, array $files, string $to)
-    {
-        foreach ($manifest as $source => $target) {
-            $target = $this->options->expandTargetDir($target);
-
-            if ('.git' === $target) {
-                // never remove the main Git directory, even if it was created by a recipe
-                continue;
-            }
-
-            if ('/' === substr($source, -1)) {
-                foreach (array_keys($files) as $file) {
-                    if (str_starts_with($file, $source)) {
-                        $this->removeFile($this->path->concatenate([$to, $target, substr($file, \strlen($source))]));
-                    }
-                }
-            } else {
-                $this->removeFile($this->path->concatenate([$to, $target]));
-            }
-        }
-    }
-
     private function removeFile(string $to)
     {
         if (!file_exists($to)) {
diff --git a/src/Flex.php b/src/Flex.php
index d1f36bf6..fdaaf003 100644
--- a/src/Flex.php
+++ b/src/Flex.php
@@ -111,13 +111,19 @@ class_exists(__NAMESPACE__.str_replace('/', '\\', substr($file, \strlen(__DIR__)
         $this->composer = $composer;
         $this->io = $io;
         $this->config = $composer->getConfig();
+
+        $composerFile = Factory::getComposerFile();
+        $composerLock = 'json' === pathinfo($composerFile, \PATHINFO_EXTENSION) ? substr($composerFile, 0, -4).'lock' : $composerFile.'.lock';
+        $symfonyLock = str_replace('composer', 'symfony', basename($composerLock));
+
+        $this->lock = new Lock(getenv('SYMFONY_LOCKFILE') ?: \dirname($composerLock).'/'.(basename($composerLock) !== $symfonyLock ? $symfonyLock : 'symfony.lock'));
         $this->options = $this->initOptions();
 
         // if Flex is being upgraded, the original operations from the original Flex
         // instance are stored in the static property, so we can reuse them now.
-        if (property_exists(self::class, 'storedOperations') && self::$storedOperations) {
-            $this->operations = self::$storedOperations;
-            self::$storedOperations = [];
+        if (property_exists(Flex::class, 'storedOperations') && Flex::$storedOperations) {
+            $this->operations = Flex::$storedOperations;
+            Flex::$storedOperations = [];
         }
 
         $symfonyRequire = preg_replace('/\.x$/', '.x-dev', getenv('SYMFONY_REQUIRE') ?: ($composer->getPackage()->getExtra()['symfony']['require'] ?? ''));
@@ -130,12 +136,7 @@ class_exists(__NAMESPACE__.str_replace('/', '\\', substr($file, \strlen(__DIR__)
             $this->filter = new PackageFilter($io, $symfonyRequire, $this->downloader);
         }
 
-        $composerFile = Factory::getComposerFile();
-        $composerLock = 'json' === pathinfo($composerFile, \PATHINFO_EXTENSION) ? substr($composerFile, 0, -4).'lock' : $composerFile.'.lock';
-        $symfonyLock = str_replace('composer', 'symfony', basename($composerLock));
-
         $this->configurator = new Configurator($composer, $io, $this->options);
-        $this->lock = new Lock(getenv('SYMFONY_LOCKFILE') ?: \dirname($composerLock).'/'.(basename($composerLock) !== $symfonyLock ? $symfonyLock : 'symfony.lock'));
 
         $disable = true;
         foreach (array_merge($composer->getPackage()->getRequires() ?? [], $composer->getPackage()->getDevRequires() ?? []) as $link) {
@@ -210,8 +211,9 @@ class_exists(__NAMESPACE__.str_replace('/', '\\', substr($file, \strlen(__DIR__)
      */
     public function deactivate(Composer $composer, IOInterface $io)
     {
-        // store operations in case Flex is being upgraded
-        self::$storedOperations = $this->operations;
+        // Using `Flex::` instead of `self::` to avoid issues when
+        // composer renames plugin classes when upgrading them
+        Flex::$storedOperations = $this->operations;
         self::$activated = false;
     }
 
@@ -707,7 +709,7 @@ private function initOptions(): Options
             'runtime' => $extra['runtime'] ?? [],
         ], $extra);
 
-        return new Options($options, $this->io);
+        return new Options($options, $this->io, $this->lock);
     }
 
     private function formatOrigin(Recipe $recipe): string
diff --git a/src/Options.php b/src/Options.php
index ee0bb3b3..55aeae7a 100644
--- a/src/Options.php
+++ b/src/Options.php
@@ -22,11 +22,13 @@ class Options
     private $options;
     private $writtenFiles = [];
     private $io;
+    private $lockData;
 
-    public function __construct(array $options = [], ?IOInterface $io = null)
+    public function __construct(array $options = [], ?IOInterface $io = null, ?Lock $lock = null)
     {
         $this->options = $options;
         $this->io = $io;
+        $this->lockData = $lock?->all() ?? [];
     }
 
     public function get(string $name)
@@ -101,6 +103,38 @@ public function shouldWriteFile(string $file, bool $overwrite, bool $skipQuestio
         return $this->io && $this->io->askConfirmation(\sprintf('File "%s" has uncommitted changes, overwrite? [y/N] ', $name), false);
     }
 
+    public function getRemovableFiles(Recipe $recipe, Lock $lock): array
+    {
+        if (null === $removableFiles = $this->lockData[$recipe->getName()]['files'] ?? null) {
+            $removableFiles = [];
+            foreach (array_keys($recipe->getFiles()) as $source => $target) {
+                if (str_ends_with($source, '/')) {
+                    $removableFiles[] = $this->expandTargetDir($target);
+                }
+            }
+        }
+
+        unset($this->lockData[$recipe->getName()]);
+        $lockedFiles = array_count_values(array_merge(...array_column($lock->all(), 'files')));
+
+        $nonRemovableFiles = [];
+        foreach ($removableFiles as $i => $file) {
+            if (isset($lockedFiles[$file])) {
+                $nonRemovableFiles[] = $file;
+                unset($removableFiles[$i]);
+            }
+        }
+
+        if ($nonRemovableFiles && $this->io) {
+            $this->io?->writeError('    <warning>The following files are still referenced by other recipes, you might need to adjust them manually:</warning>');
+            foreach ($nonRemovableFiles as $file) {
+                $this->io?->writeError('      - '.$file);
+            }
+        }
+
+        return array_values($removableFiles);
+    }
+
     public function toArray(): array
     {
         return $this->options;
diff --git a/tests/Configurator/CopyFromRecipeConfiguratorTest.php b/tests/Configurator/CopyFromRecipeConfiguratorTest.php
index 95f01656..2d6ba3c5 100644
--- a/tests/Configurator/CopyFromRecipeConfiguratorTest.php
+++ b/tests/Configurator/CopyFromRecipeConfiguratorTest.php
@@ -61,7 +61,7 @@ public function testConfigureLocksFiles()
     public function testConfigureAndOverwriteFiles()
     {
         if (!file_exists($this->targetDirectory)) {
-            mkdir($this->targetDirectory);
+            @mkdir($this->targetDirectory, 0777, true);
         }
         file_put_contents($this->targetFile, '-');
         $lock = $this->getMockBuilder(Lock::class)->disableOriginalConstructor()->getMock();
@@ -99,17 +99,22 @@ public function testConfigure()
     public function testUnconfigureKeepsLockedFiles()
     {
         if (!file_exists($this->sourceDirectory)) {
-            mkdir($this->sourceDirectory);
+            @mkdir($this->sourceDirectory, 0777, true);
+        }
+        if (!file_exists($this->targetDirectory)) {
+            @mkdir($this->targetDirectory, 0777, true);
         }
+        file_put_contents($this->targetFile, '');
         file_put_contents($this->sourceFile, '-');
-        $this->assertFileExists($this->sourceFile);
 
         $lock = new Lock(FLEX_TEST_DIR.'/test.lock');
-        $lock->set('other-recipe', ['files' => ['./'.$this->targetFileRelativePath]]);
+        $lock->set('other-recipe', ['files' => [$this->targetFileRelativePath]]);
 
+        $this->recipe->method('getName')->willReturn('test-recipe');
         $this->createConfigurator()->unconfigure($this->recipe, [$this->targetFileRelativePath], $lock);
 
         $this->assertFileExists($this->sourceFile);
+        $this->assertFileExists($this->targetFile);
     }
 
     public function testUnconfigure()
@@ -118,11 +123,12 @@ public function testUnconfigure()
         $this->io->expects($this->at(1))->method('writeError')->with(['      Removed <fg=green>"./config/file"</>']);
 
         if (!file_exists($this->targetDirectory)) {
-            mkdir($this->targetDirectory);
+            @mkdir($this->targetDirectory, 0777, true);
         }
         file_put_contents($this->targetFile, '');
         $this->assertFileExists($this->targetFile);
         $lock = $this->getMockBuilder(Lock::class)->disableOriginalConstructor()->getMock();
+        $this->recipe->method('getName')->willReturn('test-recipe');
         $this->createConfigurator()->unconfigure($this->recipe, [$this->targetFileRelativePath], $lock);
         $this->assertFileDoesNotExist($this->targetFile);
     }
@@ -270,8 +276,6 @@ public function testUpdateResolveDirectories()
 
     protected function setUp(): void
     {
-        parent::setUp();
-
         $this->sourceDirectory = FLEX_TEST_DIR.'/source';
         $this->sourceFileRelativePath = 'source/file';
         $this->sourceFile = $this->sourceDirectory.'/file';
@@ -294,14 +298,16 @@ protected function setUp(): void
 
     protected function tearDown(): void
     {
-        parent::tearDown();
-
         $this->cleanUpTargetFiles();
     }
 
     private function createConfigurator(): CopyFromRecipeConfigurator
     {
-        return new CopyFromRecipeConfigurator($this->getMockBuilder(Composer::class)->getMock(), $this->io, new Options(['root-dir' => FLEX_TEST_DIR, 'config-dir' => 'config'], $this->io));
+        $lock = new Lock(FLEX_TEST_DIR.'/test.lock');
+        $lock->set('test-recipe', ['files' => [$this->targetFileRelativePath]]);
+        $options = new Options(['root-dir' => FLEX_TEST_DIR, 'config-dir' => 'config'], $this->io, $lock);
+
+        return new CopyFromRecipeConfigurator($this->getMockBuilder(Composer::class)->getMock(), $this->io, $options);
     }
 
     private function cleanUpTargetFiles()