Hmm, I only seem to remember there being an 'EDDI.sqlite' file that stores all system data for the systems you've visited (plus some you haven't), and a few other bits and pieces. I don't remember there being any other .sqlite files. But I could wrong, as I haven't really looked at that side of EDDI until the last year or so. I'm sure
@T'kael will be able to provide a proper answer to your questions.
As for log location, they are stored in %AppData%\Roaming\EDDI as the default location.
Ah, this is for when the EDDI.sqlite file sometimes seems to 'go out of sync' with scanning systems. Here's an excerpt from the readme for the repair tool, that better explains it:
"
... to repair missing (null) 'systemAddress' data for bodies and fixed stations (orbital and surface) in the EDDI database. It will also attempt to repair missing (null) 'systemaddress' field data. This one is different to that of bodies and stations, and seems to be a key field for systems in the database. These can sometimes be missing due to them being old (before this information existed?) or due to errors in the database."
EDIT: I've just found an old back-up of EDDI from 2017 (version 2.1.0) that I have laying around (don't ask!), and that also only has an EDDI.sqlite file, no other .sqlite files. I don't know if older versions of EDDI had the files you mention though.