I would be careful going forward for the sake of protecting your data. In that case I would definitely reach out to ESRI technical support to protect existing data. They're great on topics like this. One workflow I can think of would be to export and save all data in a format that can be imported later (if that would be possible to import), and publish the edits only then. Since it sounds like there are the needs to results would need to be brought in anyways, I would export a hard save of the existing data regardless.
Happy to help, I'm sure I'll get to the point you're at soon enough on my projects. Best regards, J.Lyons