Did you look into Settings, Library, Skipped files? Re-import everything and look in there and it will tell you what the skipped files are and why they were skipped. That will give you a clue as to what is going on. It may be files Roon sees as corrupt or, if you have a lot of MP3 or AAC files it could be a codec issue.
Thank you for the suggestion, but this issue is now a moot point. I installed an internal SSD. I used the same source disk for the audio files as for the USB HDD, and the SSD is just fine. So it seems there are some problems with reading external (USB) exFAT HDDs.
OK, no problem. Glad you have a solution.