diff --git a/platform/platform-tests/testSrc/com/intellij/execution/wsl/WslSyncTest.kt b/platform/platform-tests/testSrc/com/intellij/execution/wsl/WslSyncTest.kt
index dc019d673a53..55ac09c5da48 100644
--- a/platform/platform-tests/testSrc/com/intellij/execution/wsl/WslSyncTest.kt
+++ b/platform/platform-tests/testSrc/com/intellij/execution/wsl/WslSyncTest.kt
@@ -302,6 +302,36 @@ class WslSyncTest(private val linToWin: Boolean) {
     )
   }
 
+  @Test
+  fun testRetainUnmatchedFiles() = runWithJob {
+    val windowsDir = winDirRule.newDirectoryPath()
+    val srcDir = if (linToWin) linuxDirAsPath else windowsDir
+    val dstDir = if (linToWin) windowsDir else linuxDirAsPath
+
+    val sourceFiles = listOf("file1.txt", "file2.txt", "file3.txt")
+    for (fileName in sourceFiles) {
+      srcDir.resolve(fileName).writeText("Content of $fileName")
+    }
+
+    val extraFile = "extra_file.txt"
+    dstDir.resolve(extraFile).writeText("Content of $extraFile")
+    WslSync.syncWslFolders(linuxDirRule.dir, windowsDir, wslRule.wsl, linToWin, retainUnmatchedFiles = false)
+    Assert.assertFalse("Extra file should be deleted", dstDir.resolve(extraFile).exists())
+    dstDir.resolve(extraFile).writeText("Content of $extraFile")
+
+    WslSync.syncWslFolders(linuxDirRule.dir, windowsDir, wslRule.wsl, linToWin, retainUnmatchedFiles = true)
+
+    for (fileName in sourceFiles) {
+      Assert.assertTrue("Source file $fileName should be present", dstDir.resolve(fileName).exists())
+    }
+
+    Assert.assertTrue("Extra file should be retained", dstDir.resolve(extraFile).exists())
+
+    Assert.assertEquals("Content of extra file should be unchanged",
+                        "Content of $extraFile",
+                        dstDir.resolve(extraFile).readText())
+  }
+
   @Test
   fun syncWithIncludesAndStubs() = runWithJob {
     doSyncAndAssertFilePresence(
diff --git a/platform/wsl-impl/src/com/intellij/execution/wsl/sync/WslSync.kt b/platform/wsl-impl/src/com/intellij/execution/wsl/sync/WslSync.kt
index 6c503237b624..ee8950311f93 100644
--- a/platform/wsl-impl/src/com/intellij/execution/wsl/sync/WslSync.kt
+++ b/platform/wsl-impl/src/com/intellij/execution/wsl/sync/WslSync.kt
@@ -129,22 +129,22 @@ class WslSync<SourceFile, DestFile> private constructor(private val source: File
       val sourceHashAndName = sourceHashes[destRecord.fileLowerCase]
 
       if (sourceHashAndName != null) {
-        if (sourceHashAndName.hash == destRecord.hash) {
-          sourceHashes.remove(destRecord.fileLowerCase)
-        } else {
-          destFilesToRemove.add(destRecord.file)
-        }
-      } else {
-        if (!retainUnmatchedFiles) {
-          destFilesToRemove.add(destRecord.file)
+        if (sourceHashAndName.hash != destRecord.hash) {
+          filesToCopy.add(sourceHashAndName.file)
         }
+        sourceHashes.remove(destRecord.fileLowerCase)
+      } else if (!retainUnmatchedFiles) {
+        destFilesToRemove.add(destRecord.file)
       }
     }
 
+    // Add remaining files from source that don't exist in dest
     filesToCopy.addAll(sourceHashes.values.map { it.file })
-    copyFilesInParallel(filesToCopy)
 
-    if (!retainUnmatchedFiles) { dest.removeFiles(destFilesToRemove) }
+    copyFilesInParallel(filesToCopy)
+    if (!retainUnmatchedFiles) {
+      dest.removeFiles(destFilesToRemove)
+    }
 
     syncLinks(sourceSyncData.links, destSyncData.links)
     syncStubs(sourceSyncData.stubs, destSyncData.stubs)