I have an example of a type of set (parent/clone) in which CLRMAME might not be acting as intended. The combination I'm looking at are the sets SCI and SCIJ. There is a certain file which share CRC/MD5 - but have different filenames.

In SCI, there is a file named: c09-14.42, which is needed also by SCIJ, but with a different filename: c09-10.42.
Unless I have a mis-checked or an unchecked setting - CLRMAME is putting a copy of this file into the SCIJ.zip rather than letting me use the parent SCI.zip which contains the correct rom (though, again, it's named differently). This is using Split Set format, not a Merged Set.