diff --git a/python/python-sdk/src/com/jetbrains/python/sdk/PythonSdkAdditionalData.java b/python/python-sdk/src/com/jetbrains/python/sdk/PythonSdkAdditionalData.java
index edd740711386..f1af77fe25d1 100644
--- a/python/python-sdk/src/com/jetbrains/python/sdk/PythonSdkAdditionalData.java
+++ b/python/python-sdk/src/com/jetbrains/python/sdk/PythonSdkAdditionalData.java
@@ -11,6 +11,7 @@ import com.intellij.openapi.projectRoots.Sdk;
 import com.intellij.openapi.projectRoots.SdkAdditionalData;
 import com.intellij.openapi.util.JDOMExternalizer;
 import com.intellij.openapi.util.io.FileUtil;
+import com.intellij.openapi.util.io.NioPathUtil;
 import com.intellij.openapi.util.text.StringUtil;
 import com.intellij.openapi.vfs.LocalFileSystem;
 import com.intellij.openapi.vfs.VirtualFile;
@@ -274,9 +275,10 @@ public class PythonSdkAdditionalData implements SdkAdditionalData {
       }
     }
 
-    if (!hasValidWorkingDirectory()) {
+    if (!hasValidWorkingDirectory() || !myWorkingDirectoryIsCanonical) {
       Path workingDirectory = flavorMigration.workingDirectory();
       if (workingDirectory == null) workingDirectory = requirementsWorkingDirectory;
+      if (workingDirectory == null && hasValidWorkingDirectory()) workingDirectory = myWorkingDirectory;
       if (workingDirectory == null) workingDirectory = fallbackWorkingDirectory;
 
       if (workingDirectory != null && !workingDirectory.toString().isBlank()) {
@@ -321,6 +323,14 @@ public class PythonSdkAdditionalData implements SdkAdditionalData {
         myWorkingDirectoryIsCanonical = false;
         myMigrationRequired = true;
       }
+      else if (myAssociatedModulePath != null) {
+        Path associatedModulePath = NioPathUtil.toNioPathOrNull(myAssociatedModulePath);
+        if (associatedModulePath != null && !Objects.equals(associatedModulePath, EMPTY_WORKING_DIRECTORY)) {
+          myWorkingDirectory = associatedModulePath;
+          myWorkingDirectoryIsCanonical = false;
+          myMigrationRequired = true;
+        }
+      }
       myRequirementsFile = element.getAttributeValue(REQUIREMENTS_FILE);
       String legacyRequiredTxtPath = element.getAttributeValue(ASSOCIATED_REQUIRED_TXT_PATH);
       myLegacyRequiredTxtPath = legacyRequiredTxtPath == null ? null : Path.of(legacyRequiredTxtPath);
diff --git a/python/src/com/jetbrains/python/sdk/PythonSdkAdditionalDataMigrationActivity.kt b/python/src/com/jetbrains/python/sdk/PythonSdkAdditionalDataMigrationActivity.kt
index 314bf22b1b32..ed23957c14a2 100644
--- a/python/src/com/jetbrains/python/sdk/PythonSdkAdditionalDataMigrationActivity.kt
+++ b/python/src/com/jetbrains/python/sdk/PythonSdkAdditionalDataMigrationActivity.kt
@@ -10,6 +10,8 @@ import com.intellij.openapi.projectRoots.Sdk
 import com.intellij.openapi.roots.ModuleRootManager
 import com.intellij.openapi.roots.ProjectRootManager
 import com.intellij.openapi.startup.ProjectActivity
+import com.intellij.platform.backend.workspace.WorkspaceModel
+import com.intellij.platform.backend.workspace.impl.WorkspaceModelInternal
 import com.intellij.util.concurrency.annotations.RequiresWriteLock
 import org.jetbrains.annotations.ApiStatus
 import java.nio.file.Path
@@ -19,6 +21,10 @@ class PythonSdkAdditionalDataMigrationActivity : ProjectActivity, DumbAware {
   override suspend fun execute(project: Project) {
     if (project.isDisposed) return
 
+    @Suppress("UnsafeOpenServiceCast")
+    (WorkspaceModel.getInstance(project) as WorkspaceModelInternal).awaitSynchronizationWithJpsModel()
+    if (project.isDisposed) return
+
     val pythonSdks = ProjectJdkTable.getInstance().allJdks.filter { PythonSdkUtil.isPythonSdk(it) }
     writeAction {
       migratePythonSdkAdditionalData(project, pythonSdks)