I don't know if you still check this or not but I'm having an interesting problem...
I have a Sapphire save file that is saved right before the Elite Four and I can edit the save and have no problems with it but once I beat the Elite Four and after the game resets due to beating the Elite Four, I can no longer edit the save.
I do the same thing of exporting the battery file, editing the save, and then importing but it just defaults back to a previous save. The interesting part is after I beat the Elite Four and open the save file via A Save, it asks me what game is this for, "R/S, FR/LG, E" but it does not do that on my save file before I beat the Elite Four.