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I started playing FFX a few months ago but then with exams and stuff i stopped playing. That was a few months ago, I never deleted PCSX2 but i did delete the iso (http://prntscr.com/b4xk5l - first folder contains the documents copy-pasted folder and the second one the emulator with the bios and stuff).

I tried running the game and this is what i got for both cards http://prntscr.com/b4xkmx
Went to the memory card settings and the game is indeed in there http://prntscr.com/b4xl5w so i dont understand why its not working
Quick save files also don't work saying there's no save file while there actually is http://prntscr.com/b4xlok
I'm aware that it could be a problem of it being a different ISO file but i highly doubt that is the case. 
I've done this many times with FFIX with my ps1 emulator and it works perfectly, so is there a way to fix whatever is happening with these save files?

Please post the contents of the emulog.txt file after the problem occurs. The file can be found in "My Documents\PCSX2\logs" for the installer version or in "PCSX2\logs" for the portable/binary version.

If you are now trying a different region of the same game (for example either the NTSC version or a different PAL version for example international), the saves will not work and that's normal.