Windows – How to tell between FAT16 and FAT32 USB? (Windows)

Yes, you can. But be aware that FAT32 has a limited file size: one single file can be no more then 4 GB, while NTFS has a way bigger limit. So if you try to copy a file which has more than 4 GB from NTFS to FAT32, it will fail.

Similar limitations apply to the number of files in a single directory.

I may have found the actual Windows driver code that's causing the issue.

MS happens to include the FAT filesystem driver in a package of sample driver code. There are several places in that driver where, if the filesystem is FAT12, the driver will not bother to do something like set the dirty bit (maybe there is none for FAT12) or flush the FAT data.

https://github.com/Microsoft/Windows-driver-samples/blob/master/filesys/fastfat/verfysup.c#L774 https://github.com/Microsoft/Windows-driver-samples/blob/master/filesys/fastfat/cachesup.c#L1212 and maybe most critically: https://github.com/Microsoft/Windows-driver-samples/blob/master/filesys/fastfat/cleanup.c#L1101

In the last link, in cleanup.c, the FAT is not flushed if the filesystem is FAT12. I think this may be causing exactly the behavior I see:

    //
    //  If that worked ok,  then see if we should flush the FAT as well.
    //

    if (NT_SUCCESS(Status) && Fcb && !FatIsFat12( Vcb) && 
        FlagOn( Fcb->FcbState, FCB_STATE_FLUSH_FAT)) {

        Status = FatFlushFat( IrpContext, Vcb);

Reported to Microsoft in Windows Feedback Hub at https://aka.ms/btvdog (special URL that opens in Feedback Hub).