diff --git a/src/Command/UpdateRecipesCommand.php b/src/Command/UpdateRecipesCommand.php
index 5bd9731e..2839559e 100644
--- a/src/Command/UpdateRecipesCommand.php
+++ b/src/Command/UpdateRecipesCommand.php
@@ -193,7 +193,7 @@ protected function execute(InputInterface $input, OutputInterface $output): int
                 '  After resolving, commit your changes like normal.',
             ]);
         } else {
-            if (!$patch->getPatch()) {
+            if (!$patch->getPatch() && !$patch->getDeletedFiles()) {
                 // no changes were required
                 $io->write([
                     '  No files were changed as a result of the update.',
diff --git a/src/Update/RecipePatch.php b/src/Update/RecipePatch.php
index bb6abdbc..4828a6ed 100644
--- a/src/Update/RecipePatch.php
+++ b/src/Update/RecipePatch.php
@@ -17,13 +17,15 @@ class RecipePatch
     private $blobs;
     private $deletedFiles;
     private $removedPatches;
+    private $keptFiles;
 
-    public function __construct(string $patch, array $blobs, array $deletedFiles, array $removedPatches = [])
+    public function __construct(string $patch, array $blobs, array $deletedFiles, array $removedPatches = [], array $keptFiles = [])
     {
         $this->patch = $patch;
         $this->blobs = $blobs;
         $this->deletedFiles = $deletedFiles;
         $this->removedPatches = $removedPatches;
+        $this->keptFiles = $keptFiles;
     }
 
     public function getPatch(): string
@@ -49,4 +51,13 @@ public function getRemovedPatches(): array
     {
         return $this->removedPatches;
     }
+
+    /**
+     * Files removed in the recipe that were not deleted because
+     * they have been modified in the user's project.
+     */
+    public function getKeptFiles(): array
+    {
+        return $this->keptFiles;
+    }
 }
diff --git a/src/Update/RecipePatcher.php b/src/Update/RecipePatcher.php
index 66965ee0..c04f6d23 100644
--- a/src/Update/RecipePatcher.php
+++ b/src/Update/RecipePatcher.php
@@ -46,10 +46,6 @@ public function applyPatch(RecipePatch $patch, ?string $packageName = null): boo
 
         $nonRemovableFiles = [];
         foreach ($patch->getDeletedFiles() as $deletedFile) {
-            if (!file_exists($this->rootDir.'/'.$deletedFile)) {
-                continue;
-            }
-
             if (isset($lockedFiles[$deletedFile])) {
                 $nonRemovableFiles[] = $deletedFile;
 
@@ -68,6 +64,15 @@ public function applyPatch(RecipePatch $patch, ?string $packageName = null): boo
             $this->io->writeError('');
         }
 
+        if ($patch->getKeptFiles()) {
+            $this->io->writeError('  <warning>The following files were removed in the recipe, but they were kept because you modified them. You might need to remove them manually:</warning>');
+            foreach ($patch->getKeptFiles() as $file) {
+                $this->io->writeError('      - '.$file);
+            }
+
+            $this->io->writeError('');
+        }
+
         return $withConflicts;
     }
 
@@ -85,12 +90,25 @@ public function generatePatch(array $originalFiles, array $newFiles): RecipePatc
         }, \ARRAY_FILTER_USE_BOTH);
 
         $deletedFiles = [];
-        // find removed files & record that they are deleted
+        $keptFiles = [];
+        // find removed files & record that they are deleted, unless they were modified in the project
         // unset them from originalFiles to avoid unnecessary blobs being added
         foreach ($originalFiles as $file => $contents) {
-            if (!isset($newFiles[$file])) {
+            if (isset($newFiles[$file])) {
+                continue;
+            }
+
+            unset($originalFiles[$file]);
+
+            $path = $this->rootDir.'/'.$file;
+            if (!file_exists($path)) {
+                continue;
+            }
+
+            if (file_get_contents($path) === $contents) {
                 $deletedFiles[] = $file;
-                unset($originalFiles[$file]);
+            } else {
+                $keptFiles[] = $file;
             }
         }
 
@@ -136,7 +154,8 @@ public function generatePatch(array $originalFiles, array $newFiles): RecipePatc
                 $patchString,
                 $blobs,
                 $deletedFiles,
-                $removedPatches
+                $removedPatches,
+                $keptFiles
             );
         } finally {
             try {
diff --git a/tests/Update/RecipePatchTest.php b/tests/Update/RecipePatchTest.php
index 97f28769..dd98ce41 100644
--- a/tests/Update/RecipePatchTest.php
+++ b/tests/Update/RecipePatchTest.php
@@ -22,12 +22,14 @@ public function testBasicFunctioning()
         $blobs = ['blob1', 'blob2', 'beware of the blob'];
         $deletedFiles = ['old_file.txt'];
         $removedPatches = ['foo' => 'some diff'];
+        $keptFiles = ['modified_file.txt'];
 
-        $patch = new RecipePatch($thePatch, $blobs, $deletedFiles, $removedPatches);
+        $patch = new RecipePatch($thePatch, $blobs, $deletedFiles, $removedPatches, $keptFiles);
 
         $this->assertSame($thePatch, $patch->getPatch());
         $this->assertSame($blobs, $patch->getBlobs());
         $this->assertSame($deletedFiles, $patch->getDeletedFiles());
         $this->assertSame($removedPatches, $patch->getRemovedPatches());
+        $this->assertSame($keptFiles, $patch->getKeptFiles());
     }
 }
diff --git a/tests/Update/RecipePatcherTest.php b/tests/Update/RecipePatcherTest.php
index 1b51e957..5a460355 100644
--- a/tests/Update/RecipePatcherTest.php
+++ b/tests/Update/RecipePatcherTest.php
@@ -11,6 +11,7 @@
 
 namespace Symfony\Flex\Tests\Update;
 
+use Composer\IO\BufferIO;
 use Composer\IO\IOInterface;
 use PHPUnit\Framework\Attributes\DataProvider;
 use PHPUnit\Framework\TestCase;
@@ -37,10 +38,7 @@ public function testGeneratePatch(array $originalFiles, array $newFiles, string
         self::getFilesystem()->mkdir(FLEX_TEST_DIR);
         // original files need to be present to avoid patcher thinking they were deleting and skipping patch
         foreach ($originalFiles as $file => $contents) {
-            touch(FLEX_TEST_DIR.'/'.$file);
-            if ('.gitignore' === $file) {
-                file_put_contents(FLEX_TEST_DIR.'/'.$file, $contents);
-            }
+            file_put_contents(FLEX_TEST_DIR.'/'.$file, $contents ?? '');
         }
 
         // make sure the test directory is a git repo
@@ -195,6 +193,45 @@ public function testGeneratePatchOnDeletedFile()
         $this->assertSame('', $patch->getPatch());
     }
 
+    public function testDeletedFileModifiedInAppIsKept()
+    {
+        (new Process(['git', 'init'], FLEX_TEST_DIR))->mustRun();
+        (new Process(['git', 'config', 'user.name', 'Unit test'], FLEX_TEST_DIR))->mustRun();
+        (new Process(['git', 'config', 'user.email', ''], FLEX_TEST_DIR))->mustRun();
+
+        $dir = FLEX_TEST_DIR.'/config/packages';
+        @mkdir($dir, 0777, true);
+        $modifiedContents = <<<YAML
+            framework:
+                workflows:
+                    blog_publishing:
+                        places: [draft, published]
+            YAML;
+        file_put_contents($dir.'/workflow.yaml', $modifiedContents);
+        file_put_contents($dir.'/untouched.yaml', '# untouched');
+        (new Process(['git', 'add', '-A'], FLEX_TEST_DIR))->mustRun();
+        (new Process(['git', 'commit', '-m', 'Committing original files'], FLEX_TEST_DIR))->mustRun();
+
+        $io = new BufferIO();
+        $patcher = new RecipePatcher(FLEX_TEST_DIR, $io, $this->createStub(Lock::class));
+
+        $patch = $patcher->generatePatch([
+            'config/packages/workflow.yaml' => "framework:\n    workflows: null\n",
+            'config/packages/untouched.yaml' => '# untouched',
+            'config/packages/missing.yaml' => '# missing',
+        ], []);
+
+        $this->assertSame('', $patch->getPatch());
+        $this->assertSame(['config/packages/untouched.yaml'], $patch->getDeletedFiles());
+        $this->assertSame(['config/packages/workflow.yaml'], $patch->getKeptFiles());
+
+        $this->assertTrue($patcher->applyPatch($patch));
+        $this->assertSame($modifiedContents, file_get_contents($dir.'/workflow.yaml'));
+        $this->assertFileDoesNotExist($dir.'/untouched.yaml');
+        $this->assertSame("D  config/packages/untouched.yaml\n", (new Process(['git', 'status', '--porcelain'], FLEX_TEST_DIR))->mustRun()->getOutput());
+        $this->assertStringContainsString("they were kept because you modified them. You might need to remove them manually:</warning>\n      - config/packages/workflow.yaml\n", $io->getOutput());
+    }
+
     #[DataProvider('provideApplyPatchCases')]
     public function testApplyPatch(array $filesCurrentlyInApp, RecipePatch $recipePatch, array $expectedFiles, bool $expectedConflicts)
     {
@@ -451,7 +488,7 @@ public function testIntegration(bool $useNullForMissingFiles)
         $this->assertSame($files['dot_env_clean']['expected'], file_get_contents(FLEX_TEST_DIR.'/.env'));
         $this->assertSame($files['package_json_conflict']['expected'], file_get_contents(FLEX_TEST_DIR.'/package.json'));
         $this->assertSame($files['webpack_encore_added']['expected'], file_get_contents(FLEX_TEST_DIR.'/config/packages/webpack_encore.yaml'));
-        $this->assertFileDoesNotExist(FLEX_TEST_DIR.'/security.yaml');
+        $this->assertFileDoesNotExist(FLEX_TEST_DIR.'/config/packages/security.yaml');
     }
 
     public static function getIntegrationTests(): iterable