From what I've read on posts here, the GBA saves don't actually save to your m3 until you turn the system off and turn it back on. When you turn it back on it moves that save from the GBA expansion pack to the M3. Not long ago someone was saying they believe the save deletes occur for one of two reasons.
1: You play GBA game A, save, turn it off and remove the expansion pack before turning it on again.
2: You play GBA game A, save, turn it off then on (so it saves to m3) but then before actually running anything else you turn it off remove expansion pack and when you turn the system back on it sees the last thing you did was play said GBA game so it tries to copy to save from the expansion pack (which isn't there so it's blank) and erases your save.
I haven't used my expansion pack much, but this is what I've picked up from other peoples posts over time. Anyone feel free to correct me.
So just make sure when you play a GBA game to shut the system down after your done, turn it back on, then run some other game (prolly homebrew or an NDS game) before turning it off again.