Welcome to the forum!
It seems unlikely that most of the "missing" files are actually MP3 files, considering that the difference in data size is only .13 GB. Do you have lyrics or artwork files in that folder? I notice that some of MB's settings files are shown in the screenshot. If there are other settings files we're not seeing, they may account for the difference in number of files.
As for the file in your Inbox, the physical location of the file doesn't matter to MB. It only knows which files you've told it go in the Library. If you move the stray file from Inbox to Library, the location won't change unless you have Auto-Organize enabled.
It is likely that the replacement file also got scanned into the inbox, which is what MB does with new files by default. If that's not the case, have you tried just dragging and dropping it straight into the inbox or library?
Hello and thank you for the greeting, this seems like a lovely forum!
There are album art files within folders, although most of the album art is embedded into the songs themselves (does that count as a file separate from the mp3) however I suppose this could explain the difference in the amount of files.
For the two missing files, i'm not concerned about them being part of the MB size, just the fact that they aren't detected in the library scan when they are located in the folder MusicBee uses for my library. The other song did seem to have shown up in my library now (it didn't yesterday)
Forgive my ignorance, but whenever I add new music to the folder and I scan for them they always get added to the library, so why would these two get added to the inbox? Would dragging and dropping them from my inbox to the library fix the problem?