This age old problem still persists. Can you please fix this once and for all?
The simples workaround is to script SplitDisjoinedMesh into the boolean operation and then join back up the result @piac even a simple fix like that would go a long way for us, so we don’t have to manually fix this every time.
Make sure you cover overlapping geometries too then. So if we boolean a big sphere away from a small sphere, that is fully enclosed by the big sphere then the small one is deleted.
Today nothing happens. (it just deletes the big sphere)