It only prevents you from overwriting identical named but bytewise different files in case you full merge the sets.
Either it forces you to switch to "prefer split-merged" mode (if you answer NO) or it will remove the clone relationship from the set (and only from *that* set) (if you answer YES). So a minimum gain of used diskspace for that now standalone set. Noone actually cares if total MAME is around 260GB and you get some additional bytes for these sets...
If you don't want user intervention, you can set Profiler->Options->DatFile Errors->Hide Common. "Yes" is iirc the default.
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Re: I'm boycotting clrmpro.....
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Re: I'm boycotting clrmpro.....
