Steps to reproduce:

1. Create template "Template A"
2. Create template "Template B"
3. Create any item with application "App X" to "Template B"
4. "Template B" link to "Template A"
5. Export "Template A" and "Template B"
6. Update application "App X" to "App Y" in "Template B"
7. Import the exported XML with "Delete missing" option for "Applications"
   In step7, application "App X" is remained in "Template A" at step7.
8. Import the exported XML with "Delete missing" option for "Applications" again
   In step8, application "App X" is deleted in "Template A".

I think it is wrong that "App X" is not deleted in step7.