I think Hal's suggestion that the encryption state is stored elsewhere is the more probable, especially since that would also explain why your SuperDuper backup was bad too. In both cases, you recovered the raw file but didn't remove the auxiliary indication that it was supposedly encrypted.
I don't understand what that means. The only thing I understand is that, whatever the reason, I am in this situation unable to use the Time Machine backup to resolve the problem.
I just now did an experiment. I saved the file under a different name. I then replaced the original with a Time Machine copy from a month prior to the problem date. And yes, it wants the password.
The net result is that, even if the Excel design is not actually changing the TM files, the effect is the same. So, how would I or anyone else using Excel locate/remove the encryption state?
ryck