I have not tested this myself, so I'm not 100% certain. That being said, I would be surprised if change stage removed a problem flow assignment. Without knowing what the problem was, it would seem to me to be a bad idea to remove an assignment that exists to have someone review an issue and take corrective action. Potentially, when you review it, you may feel that no action is required because the change stage got you where you need to be, in which case you can close things out from within the problem flow.
OOTB FlowProblems flow rule is always initiated as a parallel flow. Stage change can clean up your Business process related pending assignments, but can't close any of the parallel flow, including FlowProblems.