The records related to what you've done (like how many you've caught, how many you've evolved, etc), the daycare, and the fusion mons were the most obvious entries.
So all I did was replace those from your main-new. Didn't even need to do anything else.
So your PC, Party, trainer data, story flags should all be the same.
Potentially your SD could be corrupt, since if you did a regular extraction and SD transfer, the save should normally be fine.
Glad to help, no worries.