Is there a Emerald equivalent or is it just Ruby and Sapphire or what Ruri calls it Saphiya
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Gaming Heaven
Nebulon_Galaxy
ciro64
I'm really sorry. 
Cheela
i remember having that issue on fire emblem 6 a long time ago, and the saviour was... VBA-M, you can import battery savefile that sometimes fixxes incompatibility between patches. You can give it a shot if you still have the files!
Scotty
@Nebulon_Galaxy It's all of Gen 3.
Here's some pre-patched ROMS (courtesy of yours truly) in case any of you are interested in playing it: https://drive.google.com/drive/folders/12ZyC_Mh3lxE9hYkNWAfgA9bEBDv0pNLB?usp=drive_link
(Try this instead; Apply these patches to a vanilla RSE & FR LG ROM: https://drive.google.com/drive/folders/17cd3pn2qtwjRva4yHOOceWafMbojA-PZ )
Here's some pre-patched ROMS (courtesy of yours truly) in case any of you are interested in playing it: https://drive.google.com/drive/folders/12ZyC_Mh3lxE9hYkNWAfgA9bEBDv0pNLB?usp=drive_link
(Try this instead; Apply these patches to a vanilla RSE & FR LG ROM: https://drive.google.com/drive/folders/17cd3pn2qtwjRva4yHOOceWafMbojA-PZ )
MasterEn
as long as the rom and save file have the same name, it should still work. i did this a couple of times while checking some stuff out for some games.
if that doesn't work, then try the import battery option that cheela said. i've done that too and it worked.
and if that doesn't work, then play some pikmin and slaughter all of the native creatures on PNF-404. that helps me out when i get frustrated. or draw some hot anime babes. that works too.
another option is using a randomizer on the games. it works on most versions of moemon. you can start again with a lot of new mons in play too. and the shiny cheat code works on the hacks too. i'll look for my screenshot of a normal shiny that i found while playing mega moemon fire red. it was a very cute moemon.
if that doesn't work, then try the import battery option that cheela said. i've done that too and it worked.
and if that doesn't work, then play some pikmin and slaughter all of the native creatures on PNF-404. that helps me out when i get frustrated. or draw some hot anime babes. that works too.
another option is using a randomizer on the games. it works on most versions of moemon. you can start again with a lot of new mons in play too. and the shiny cheat code works on the hacks too. i'll look for my screenshot of a normal shiny that i found while playing mega moemon fire red. it was a very cute moemon.