On FreeCAD 0.14 i see additional feature/check was added and probably this was added to contain integrity of the part/assembly? I do see a point in adding this feature but i must say it's quite limiting at times. I usually add/delete some circles in sketch that was already extruded to add or remove a hole and adding circles is not problematic but trying to delete one is not possible anymore?This object is referenced by other objects and thus cannot be deleted.
Today i did one part that took quite a few steps to get it right and i had to remove one hole i did at the beginning of the process by editing sketch and this is not possible anymore. Basically the only real solution would be to delete everything and start from scratch if i didn't want to use some "hacks" like new sketch on the surface and extrude to fill the existing hole? Quite frustrating because user has to know exactly down to each hole at the beginning of the process to not create one to many... I am quite sure this will cause real issues/frustrations for a lot of FreeCAD users!