Thanks BIOS-D, that image showing the difference between "non-merged / merged / split" makes it very clear.
So when CMP says; Issue: Can't merge set due to equal names for different ROM hashes Press yes to remove parent/clone relationship or no to force split-merge mode.
I assume this means that CMP can't do 'merged' so wants to know wether to do 'non-merged' or 'split'. I would personally prefer 'split' because refering to the picture 'non-merged' mode would increase the HDD space requirements for ROM storage which should also be a factor for some people.