You have a full dado on the deck. When the cabinet is regened after adjusting the stretcher, the full dado comes back. Currently, system cuts and construction are keep separate from PE cuts. So you may cut say away a part of a tenon when in the PE, but when the cabinet is regened the cut(s) to the tenon will be removed. Basically you can not maintain any cuts made by the PE on tenons (full/blind/lockdado) during a regen. You only lose those cuts (cuts outside the raw part aka cuts on tenons) when you regen. If you make those cuts the final thing you do to the cabinet you will be ok when you go to nest.
I found out the same thing when trying to add nail hole pilot holes to the backs of my cabinets. I took the back into PE and placed 1/16" holes around the edge of the back where it overlaps the sides (full dado). When I regen'd the cabinet they would disappear.
Rick told me the same thing a week or two ago. I made a hole pattern for my nail pilot holes and saved them in the contour editor, then the last thing I do before sending cabs to nesting is to apply the holes to the back and save the cabinet. The holes show up fine in the nesting when I used this approach.
Thanks, Rick, for clearing this up to me awhile back and again in this post. This might be something to include in the help files and tutorials that Dennis makes.