ROMs removed. Only upload save files.
Save in-game, and do not use save states to archive your game progress.
If other save file editors (like PokeGen) do not open them, then it is not an issue with the editors, it is an issue with your emulator/usage resulting in incorrect/improperly formatted save data.
Emulators that handle save data differently (like changing the file size by appending a footer, or compressing the data) do not get recognized by editors that lack handling for that; oftentimes, an emulator doing strange things isn't something a save editor should be responsible to handle. If programs don't get updated to handle the weird emulator formats, then you must convert them to the standard format prior to using the editor in question.