I think I have found the reason now. There have been a few recent crash reports where the application was force-quit by the user because it was so slow during the initial scan. Judging by the activity in the log, there have been a lot of edited images involved, and, with the very recent external editing improvements in 1.0.0-rc.28, those edited files are now retrospectively associated with their originals during the scan.
Since this process was never meant to work for large numbers of added files at once, I’ll probably just look for a way to disable the detection during the initial scan, as well as when adding new scanned folders.