JKSV Backup issues and PKHex

[Starrcade95]

Hi all, First post on the forum;

I have an (unpatched, HAC-001) switch that is soft-modded with Hetake/EmuMMC CFW--I am trying to back up my most recent save of Brilliant Diamond to mod it in PKHex, However, everytime I do this within JKSV, it is backing up a much older save file from March where I am in Floraroma town and not the current save where I am in Victory Road. I was able to do this beforehand with saves done after floraroma town--is there something I am doing wrong, or should this be on SysCFW?