I’m glad things returned to the prior sanity-with-oddity. Manual file deletions in the destination can be risky…
If these index files really bother you, I wonder if The LIST-BROKEN-FILES command can see any problems?
To a previous comment, changing the –dblock-size shouldn’t (AFAIK) change the 1-to-1 ratio with index files.
Compact also doesn’t change everything. It has lots of settings though, and can be nudged in that direction.
I still wonder if you have some empty dblock files, which I think would explain index files with nothing to index.
This could also be examined from a database point of view, but the easy path is to just live with the situation.