I am also having this problem but with part editor cuts. Everytime I change a cabinet in width I lose my part editor cuts but only on my fixed shelf. I have part editor cuts on my deck and top as well but they don't seem to be effected. I have all my holes constrained but that doesn't seem to help from losing them on my fixed shelf.
I have listed your cabinet to be reviewed as I am not seeing anything wrong with it.
Justin,
I have been trying to reproduce your issue using a Std Base Frameless with a Fixed Shelf.
Add PE cuts to the shelf, add constraints
Resize in multiple directions, and I am not getting this to happen.
Can you please post a cabinet for me to review with very simple parts. The simpler the cabinet, the easier it is to see the problems.