Lost my game? Need Help

[Zorlin Shape]

My setup:
I play the game on a raspberry pi with retroarch running a ppsspp emulator.
I modify the game on my windows pc.
My iso is a custom patched version (not a ton of huge changes, mainly the slowdown fix and a couple other things like move-find always finding the rare item).

What I was trying to do:
I'm near the end of the game so I wanted to use lion editor to get the multiplayer items since there is no other way to get them.

My method:
I downloaded "Linux File Systems for Windows by Paragon Software" and put my raspberry pi/retroarch sd card into my pc and loaded into the files.
I took out FFTA.sys, renamed it, added the items I wanted as buyable in the poacher's den, saved, renamed the file.
I should mention here that my retroarch ppsspp ini file already has encrypt set to false because this isn't my first time messing around with the game.

The problem:
No matter what I did I could not get the changes to recognize when I put the sd card back in the pi and booted the game. I tried a bunch of times.
(A solution for the above problem would be nice but here is my real problem...)
The last time I tried the game says that no save data could be found. I restored my backup FFTA.SYS file (that I made at the beginning and had never messed with) and even that can't be found.
I can SEE the save game file by going into the ppsspp settings game save manager. It's there. But the War of the Lions iso will not see it any longer.

Anything I can try? Anything I can do?

Thank you in advance.