What does qSlicerSegmentEditorScissorsEffectPrivate::paintApply method does in qSlicerSegmentEditorScissorsEffect.cxx ?
The method adds the painted region to the current segment and removes it from all other segments (taking into account masking settings).
How to remove it from all other segments?
You can attach a debugger and step through the code to see how it is done exactly. It is a very complex process because segments are stored in multiple layers in a 4D array and there are several masking options.
Can you for me some ideas when I crop by operation: fill inside, shape: free-form and slice cut: unlimited?