There are multiple use-cases that will cause this problem. All of them result in the overrides on sub-workflows being removed and lost. All overrides can be affected by this problem.
If you then Check Out only the Parent workflow , Check it in and deploy again the overrides on the sub-workflows are gone. The key to this is if you ONLY check out the parent workflow and check it back in and deploy the overrides on the sub workflows go away. If you Check Out both the Parent and Sub Workflows make your changes and Check them All back in and deploy then the over rides in the sub workflows work as you would think.
When importing process app blueprints in Composer, transitions inherited in sub-workflows may lose waypoints which were there before export. The conditions needed: 1) Transition must start or end on a decision
