For anyone who still uses ATR Standalone and wants to switch to MH:
You can open your save with a file editor like Notepad++ and find and replace (Ctrl + H) the changes in this commit[github.com] to migrate it.
Some things may still break, but at least it should be playable.
PS: For your sanity, ignore the backstory name changes. Those are much easier to fix with devmode in a running game.

If you need help, feel free to ask.