Far as I can tell, the choice between vmdk and vhd is a one-time-only decision during install. You can't change it after selecting one method or another. I don't believe there is a way (or at least, an official sanctioned way) to live-convert VMDK-based appstacks to VHD either. You can try one of the 3rd-party tools, but you need to have the metadata file pointing to the vhd file in order to re-import it back to App Volumes Manager. Good luck with that, I say.