My first guess would be something missing or incomplete in the metadata. Although I have no familiarity with that device, virtually all library and playing software these days rely wholly on metadata.
Are you able to view the metadata on the files on the Core? If so perhaps compare the tags of one of those that doesn’t show with another that does, to see if anything obvious is missing. If you can’t view on the Core, or if they are kept separately from the files themselves, can you copy to a computer and view the tags that way?
I have Flacbox. I had a lot of trouble trying to get it to index the 35,000 (lossy) tracks on the 512GB card attached to an iPhone 15. In the end I didn’t bother. I was comfortable relying on my folder structure to find the music I want. That may or may not be the case for you.
One thing to check is whether Flacbox has a maximum number of tracks it can index. For instance, Naim has said that in server mode its Atom can index 20,000 tracks.
That was also the limit for a Fiio DAP that I have.
The good news, however, is only yesterday on another thread, @GavinB recommended Music Streamer, which I downloaded. It appears to have indexed all 35,000 tracks - haven’t put it through a real world test yet, but how wrong can you go for $10.
Edit - AI tells me that Flacbox Premium does not have a fixed limit. But as I mentioned, I couldn’t get it to complete indexing my files. I would have tried doing the indexing in small segments, but I was OK relying on my folder structure. Also IIRC (and I’m really not certain), if I select a genre on Flacbox I simply get a list of all the tracks in that genre, not a breakdown by artist or album. That doesn’t work for me. Music Streamer lets me drill down from Genre (via a filter) to Artist to Album to Track.
Presumably in the app you need to point it at the data. Is this at a level that would exclude the Downloads folder? Perhaps it needs to be pointed at a higher level in the folder structure? (I’m not familiar with the Core folder structure.)
So i found the Achilles heel in Music Streamer - it doesn’t support UPnP/DLNA. I must say I am surprised, although it’s not a big deal as I have several other apps that will. But it’s not quite the jack of all trades I thought it was.