I did similar things from LH1 to LH2. I ran all the saves through some code which changed some behind the scenes things to make future coding easier. 
Lots of flags and checks that I ended up doing differently.
A lot of time passed between when I started LH1 to when I returned to that code. (I started LH1, then stopped to make Life of a Mobster, then back into LH1 and then into LH2).
My main goal was to keep all of the saves valid and make all of my changes be unnoticeable by the reader.
LH3 still has things being carried into it that I would do differently, but that’s the nature of a long project.