When Mame gives misleading information that two romsets should have different files with the same name within a parent/clone relationship the profiler gives the following warning:
Cloneset: 'x' uses equal names for different ROMs and so it can't be merged to its parentset: 'y'
Parent/clone relationship will be removed.

In all the cases I have checked then one of two files is a 'nodump', so there isn't a practical clash until the nodump version has been dumped.
To prevent the removal of parent/clone relationships I have removed all nodump roms from Mame's listxml output before loading it into the profiler.

Do you see any problematic side effects to this workaround?
Would you implement an option in clrmamepro to completely ignore nodump roms?

Thanks