Agree with that. The whole mod use edited original files, so using it with a new update revert the whole content of the update.
As for the errors he talk about, they are probably coming from the game itself, since the mod is really limited in what it do.
The error stems from the game itself, I believe, as my clean save shit the bed too.
Or too much cheating either through the D.S. mod and/or yours, and it bugs out the persistent state upon loading a save from a previous version.
Could be a mix of both too.
Edit: Also, resetting the hospital/nurses fixes some things too
PS; Easiest fix is just starting over, without modding anything, or replacing files though.
Eventough I uploaded the 2.0 renpy/lib for those who just do not want to start over.