Yes, at least as long as you save in plain CR2 or PZ3files - I'm not sure if it copes with compressed (CRZ) files or external binary morph targets. All it does is change hidden 0 to hidden 1 for the unused morphs.

The PBMDC and PBMCC channels aren't used for the main morphs - those channels are already named - but for add ons, DC for DAZ morphs and CC for third party (community) morphs.