OK, this worked for me previously in using the in-game save for Pokemon: FireRed, so give it a shot.
You'll need the VBA emulator for this. Some steps might be redundant, but I guess there's no harm in following them.
1. Set VBA Emulator Save Type to Auto/Flash 128K
2. Load Pokemon ROM
3. Import a compatible XPS save game (from GameFAQs)
4. It will state that save file is corrupted, but load it anyway
5. A savegame of extension *.sa1 will be generated. Change it to *.sav
6. Run the ROM through SD Patcher, importing the savegame generated previously.
7. Upload the patched files on the your SD card
8. The game will state that your save file is corrupted, but ignore it and start a new game with it. You should be able to use the in-game save from here on, despite the corrupted save file message.