Well, of course I cannot make this happen again (after seeing approximately 30 duplicates over the course of several days). The only thing I can think of that might have some bearing on the problem, is that the duplicate files had their names truncated from 36 characters to 31 characters, as noted in this thread:
https://www.mobileread.com/forums/sho...d.php?t=220936, which seems to be new behavior. I will continue to watch for this problem, and if I can make it happen again, I will write the steps down exactly to see if anyone else can replicate this problem.