I have successfully patched a CloneCD image (thanks to a prompt given by another member of this Forum). The process I used was as follows:

1 Read the original to hard disk in the normal CloneCD manner
2 Rename the IMG file to BIN and apply the patch in the normal way
3 Rename the BIN file back to IMG
4 Burne the IMG to CD-R with CloneCD

I don't guarantee all outcomes because I haven't exhaustively tested different types of patch.

But it is worth a try and a report from you on the outcome for the benefit of the Forum.