I think it's not possible to reproduce this issue if you rebuild into an empty Destination Directory.
Now my drive G:\ I always keep a Full Complete MAME romset that I update with every u cycle. My drive H:\ I only keep MAME full releases, so in this case it's 144 then 145 and skipping the u cycles.
I use only the default settings to clrmame and don't change anything. I first preform the scanner and execute new scan with all fix options checked. Then when some misses exist I jump to rebuilder and on the rebuilder I have checked the first 3 options.
compress files Zip
Recompress files
show statistics
In the rebuilder the source Directory also contains zip archives I'm always rebuilding from zipped files into a destination that also always contains zipped archives.
So far I have encountered this updating MAME ROMs and working with FBA sets. The only things in common I can think of are the destination directories have previous complete sets in them and source directory always have zip archives.
I have no idea right now if my MESS softlists are affected, but I enjoy using batch mode working with those

Thanks for everything and I wish you the best of luck at finding out how this occurs. It's really rare, but does happen and I'm completely stumped at the moment.