I had a similar problem with Pokemon Diamond on a R4 cartridge.
I was just saving my progress and mid way through the battery died. I booted the rom up after charging the DS and the game told me that the save had corrupted and that it would take me to the save point before that, luckily there wasn't too much difference. I kept saving the game but more often than not the save file would become corrupt and the game would take me back to the previous save so I had to double save all the time to kinda solve the problem (moving the sav file and renaming the rom and save didnt help either).
So the game should use the next/previous save point if the save is corrupt (and if there is a previous save), but I would just wipe the sav file from your SD card and start a new game.