Thanks again, I got a problem with the latest patched version. Importing a collection of ~65000 chiptune files of different formats (which were present in the library folder all the time) to the MB library leads to a programme crash after ~7000 files. Maybe missing supported file-extension definitions in the Configuration.xml?
On 6087, I synced ~300 s3m's, mod's, xm's, it's, mtm's (tracker modules, not necessarily chiptunes) and an album of chiptunes (12 vgm's) without issue the other day (far less than your amount, I know). Steven mentioned that some chiptunes (HES and STR) didn't play properly or not at all. Try avoiding importing problematic chiptunes, import a smaller amount at a given time (tedious, I know), etc. Report here if you run into any problematic chiptunes.
EDIT: I just imported 7,230 songs (mod, mtm, s3m, it, xm) into MB without any hiccups (again, these are tracker modules rather than chiptunes, so it may not be applicable for your situation). These songs are basically everything from hornet's demoscene archive (https://hornet.org/music/songs/