Oof, that's brutal. I think you just discovered one reason to be cautious of integrations with third-party cloud services. The fact that you're looking at mere weeks to enact your plan is...unfortunate.
If this were me and there were no good alternatives, I would identify a window of time to focus on preserving. Obviously the things that are currently in flight matter most.
My big question is: Do the decisions still exist if the document link disappears? In some respects, that's the most important because we use proof often as a means to document decisions. The details of those decisions become less and less important as time passes (arguably). I don't know the answer to my own question, so it's worth testing it or reaching out to Workfront support for guidance. If the decisions remain, then a bulk migration of the files might be what you opt to do for most items.
Workfront support also might be able to give you insights into reporting opportunities on proof decisions and comments. If you can build reports to document decision history and perhaps even comments, you can at least keep static copies in an archive. It sounds like a ton of work—not necessarily in building the reports, rather in exporting the results—but if that's what you need, it could be worth the effort.
