There *are* several roms which have identical names but different hash values within a parent/clone relationship in MAME...which would lead to some issues if you merge them manually.
So...cmpro warns you about them during data import and either removes the parent/clone relationship or forces you to split-merged/unmerged usage..depending on your selection.
Of course you can either don't care about filenames and rename them or keep clones inside (zip) subfolders of the parent ....manually.....
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Re: Will it hurt to merged sets...
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