DerMentat has mentioned multiple times that he plans to do compatibility patches, but they will only be done after this mod is 'finished' (from what I gathered, that all factions get new units).
I am positive that these patches will include version that only changes what you want to be changed, and otherwise you can ask DerMentat yourself. Though you do have to wait until the mod is finished

Ah I see, sorry didn't do my research lol. I hadn't realized that this had already been asked. Had a thought and figured i could ask. Thanks for the info!

I hope he's not too burnt out by that point.