This addon might reduce the problem: VC replaces parts by itself - #3 by andyv
However, I’m still experiencing “replaced/offset geometry” issues so I can’t really tell what to expect with the addon.
For me this bug usually happens with geometry that has been sliced, patterned or mirrored. In the pictures below the press tool ended up offset from the press, while the 2 boxes on each side of the tool remained in place.
