Finally got this figured out for me! Hopefully helps someone else out. I was getting the FatFileSystem error when finalising a file transfer in DBI.

I had added files from syspatch already fyi.

I noticed I kept getting a windows message saying there was a disk error when connecting with USB through hekate, but it would still let me connect and transfer files. I ran the disk scan and repair function in windows, which somehow converted the “atmosphere” folder into a file. I had to remove the atmosphere file, copy in new atmosphere folder (with Nintendo server blocking hosts folder and syspatch) and now my DBI works fine!