I think this is a battery problem :
I lost data in my old Pokémon version (1 or 2 years without being played) (the version hacked whith an action replay had suffer most),
My father did same with his computer motehrboard's cell (it was totally out)
and I could verify the phenomenon on a damaged N64 memory card which cell support was broken.
The easyest solution is play 1 hour every 3 month...
But if the cell is damaged... you will lost your data
Good luck...