After completing the backup I followed your earlier suggestion to copy/paste the contents of Calendar (2) into the empty Calendar file. At that point, I was able to move the two instances into the expected locations: "Calendar (2)" down to My Calendars and "Calendar" up to [main] Calendar.

I will wait a few days to make sure new appointments appear in the right instance and then delete Calendar (2).

Thanks for your help in solving this annoying problem!