MH3U - transferring a file from linux to 3DS corrupts data

While playing MH3U on Citra in Linux, the game runs fine, nothing is wrong. However, I wanted to move my save file back to my 3DS so I can play on the go, and when doing so, it corrupts the save file. I have tried checking the file multiple times, even so far as to put the 3DS “corrupted” save back into linux in another slot in MH3U, which turns out fine.

The skin turns green on both the 3DS and Windows version of Citra, as well as all items in the both weapons and items becoming corrupted. Is there something I must do to make sure the file is compatible between 3DS and Linux?