I ended up just manually determining the reference designators through net names and also by applying Instance value parameters to items where netnames were not unique enough to determine (i.e. caps on power) recording that information, creating a new sheet, copying the components from the sheet (not copying the sheet itself) then pasting the page's schematic onto the new sheet. Then deleting the "broken" sheet. I then did a layout sync and followed up by changing the reference designators on the instantiation to match what I found before.
I would still like to know if there is a better solution, or what may have caused this in the first place to avoid this happening again.