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Open VisualBoyAdvance, go to Options > Emulator > Save type > tick Flash 128k. I think that only works if the 1st save you made was with Flash 128k, as I don't think it works midway through a Flash 64k save, I could be wrong though (might aswel test it yourself, if you can keep playing your 64k file with the 128k change)
first u need 2make a yahoo ID then goin pokemongbaroms groups and download it from there Its the only place where (so far) u can download this game and where it actually saves normally.... Once u join any 1 group (there r like 5 i think..) u get a mail called file-000_readme open it and u get a list of all roms uploaded in all 5 groups search for mystery dungeon and look at the group name join that group and download its in parts ... after u get em all run the first part and u hav a rom the saves normally!!! (u can even use the wondermail)