Removing CHDs and related rom files

Hello all,
I have a question about dat files filtering.

I use DatWorkshopPro to modify the original dat file for roms, filtering it choosing "Roms only": in this way I am able to remove all CHD lines reported on dat file. However, after rebuilding my romset with ClrMamePro, a lot of unplayable roms remains, specifically the ones who requires CHDs (for example, "aliens.zip", "ddrusa.zip" and many others) because DATWorkshop has erased NOT the reference to the full game, but simply the xml lines linked to its CHD.

Do you know if DatWorkshopPro, or just ClrMamePro before rebuilding, can be set to avoid this ? Or, in second place, if a different tool exists for my purposes ?

Thank you :)