@swampwiz - I had this exact same problem on Saturday.
There are situations where the Windows registry entries for the epub (other file types too) can get corrupted so that you can't re-associate it. It's known to have been caused by a failed Calibre install - in my case I think it was related to an uninstall of 32bit Calibre that I did on Thursday last week.
Anyway I fixed it by running the CCleaner registry cleaner, I ran it several times until there were no more discrepancies.
Make sure you backup the registry before the first run. CC Cleaner will offer to do the backup, you only need to do one backup - the first one.
After 'cleaning the registry' I was able to associate the 64bit version of the viewer with the EPUB file extension.
CCleaner is not an 'aggressive' registry cleaning tool like some are. I rarely use it, but this is the second occasion its got me out of a hole in the past couple of weeks.
BR
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