I do with my saves the same way I handle my Skyrim saves:
If I change a mod, and if it isn’t a graphics mod, delete the saves and start new.
Doesn’t matter if it is a big or small mod, I’m better off starting new and avoiding a headache with unexpected bugs and crashes.
Similarly, doesn’t matter if your save is just recent or from 0.A, even a small bugfix can break your game (because that bugfix might make breaking changes, like a function typo fix).