@Fineness9996 Thanks, I will try to write a final solution posting.
I'm unsure which way you took.
a) Download Onlyoffice by removing the old CryptPad Onlyoffice folder, then replaced missing files from your backuped old Cryptpad Onlyoffice folder and finally run CryptPad upgrade procedure again. (service restart or reboot at then end?).
b) Or did you try the reinstall and migration way? (According to your postings I would say no but I don't want to write unhelpful fanatasis to close this rather long thread.)
Many thanks, glad you could solve the problem.