That is not what people mean when they say cheats potentially corrupt saves.
The mean things like by using cheats you may end up lacking a key item needed to finish the game, getting too high a score for the game to handle, getting too many items for the game to handle, or that the game tries to load the contents of your save but its contents (despite verifying OK) are not what it expected and crashes, or loads you inside a wall because cheats added an area that no longer exists because no cheats any more, or in the case of things like pokemon that pokemon you make may end up illegal and putting it all right is more effort than it is worth (or harder still if you only borrowed a mate's cheat device for a few minutes and don't have anything else to rip saves with).
GBAATM alone should have little to no bearing on emulator/flash cart loading and saving. I can think of some scenarios where it could (mainly for games that save all the time or randomly and GBAATM messed up timings or something but there are very few games on the GBA that do anything like that, and as far as I am aware Castlevania is not one of them and it would have troubled various flash carts if it did, and even then for GBAATM to mess things up there something would have to go very wrong and probably want someone to be loading hundreds of codes). There are some ROM hacks I would expect to trouble lesser emulators.
What I imagine happened here is a variation on the general theme of now you learned to always keep a backup of your save whenever you start messing around trying to convert saves between different methods. Afraid I don't know the specifics of Godmode 9 to know what went wrong, though "each identify the game differently as far as saves go" is odd. I might guess at something like Godmode 9 adds a footer or something using the game's CRC (modded game, new CRC, different game as far as it is concerned) as we saw some later third party efforts with the EZ3 in 1 do something like that and it is a reasonable way to keep your ducks in a row with GBA saves that don't necessarily have any identifying information within them to tie them back to the game.
Thanks for the clarification about corrupted game saves. Since that is the case, I decided to do a little more experimenting.
GM9 was not messing up the injecting saves!
I discovered that a couple of the cheats I was using would lose my game save!
Anytime I would enable "All Items", "All Equipment" or "Entire Competence" I would lose any previous save.
Even if I enabled it each and every time, I would start the game with no saves.
If I ignored these cheats, I could turn cheats on and off and transfer a save between copies of the game, all with no problem.
So the take away here is that ENABLING SOME CHEATS MAY ERASE YOUR SAVED GAME.
Keeping that in mind, BACKUP your save before you try any NEW CHEATS.
I can't verify that these aren't the only 3 cheats ever created that have this effect, but the potential is proven, so I, at least, intend to follow with being safe. Personally, for future games I will probably just get to the first save point. Backup my game. Then enable every single cheat I could ever consider to see if it breaks anything. If so, enable one by one till I identify the troublemaker(s).
In my case, it worked fine to start a new game with these cheats then never use them again. However, if I wanted to start a new game in another slot, I could not use those cheats again. It would erase all previously saved data. I actually would need multiple copies of the same game to do that.
The other option mentioned on this site is that I could backup my save with GM9, then use an emulator to activate those cheats, make a save there, then inject that save back onto the 3DS. (Or at least I assume this would work, if enabling those cheats via the emulator didn't cause a problem. I haven't tried it.)