For the original “non-empty blocksets with no associated blocks”, I was able to identify the likely culprits using the hints from this thread:
Using a backup of the sqlite database, I found the ones causing the original error. They are real files in the source directory, though they have some special UTF-8 foreign characters. Is it possible to just restore this sqlite database and remove those files?
Although this isn’t what is causing the current hanging issue though. I inspected my current database file and in the file view or remote view, I’m nowhere near the files that caused the "non-empty blocksets with no associated blocks”
What I’m confused about is why I don’t see anything in the live profiling log. The last statement is a select statement that runs very quickly. It doesn’t seem to indicate what is attempted to be run next. Will running the recreate command via command line give me more verbose output?