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.
Mashup Composer ... (Build 036) The Mashup online help says "You can duplicate any workflow or sub-workflow ....In the Mashup Explorer, right-click the workflow or sub-workflow , and choose Duplicate." This option is greyed out in Composer.
When deleting a transition from a workflow that has sub-workflows , an info/confirm message is displayed. When there are too many workflows, this message box does not fit into the screen, therefore it is not possible to hit the OK button. Workaround: Hit "y" to confirm or "n" to cancel.
The Allow submit on behalf of another user option appears in the Options tab of the transition Property Editor in the parent workflow's Submit transition. The option is not editable in the Submit transition in sub-workflows ; however; administrators can override this setting at the project level in SBM Application Administrator.