In the process of trying to reproduce a different problem I came across this one.
1. Take a standard cabinet from the "standard cabinets" library
2. take an END to the PE and cut a circle or really anything
3. go to the construction settings and change the TK to something different than what it was.
4. Click OK and then you will have to press OK to accept the losing of your PE cuts, but it seems only to the panels.
I had PE cuts in the backer and they didn't change.
Also, before I changed the TK settings I changed the top inset and nothing happened. I changed other settings and still nothing happened. It wasn't until I changed the TK height that my END PE cuts were lost.
This one is actually by design (or required at this time). If you add or remove a toe kick notch, the raw data point structure becomes different for the R & L ends. Because of this, we have to remove PE cuts. Note that the message reads {Any Part Editor cuts made to the Left End or Right End will be lost}. The corner cabinet parts: top, deck, and shelves are the only other parts that can fall into this situation (if you change to/from an angle/corner front or add/remove the corner gap).This is just a small caveat that must exists today.