I haven't used prime's latest creation, so can't answer that.
But whenever I flash a nightly for example, that installs kernel again that I don't use.
I will then flash the kernel I want and just let link app re setup the script.
Reboot and everything is back and linked.
A new thing I am trying is copying the data/app files that are just the links onto my sd, not wiping the ext, flashing new ROM, letting link app run script.
Reboot, make sure ext mounts by opening data/ext2 and seeing if the apps appear if not hot reboot, then recopy the data/app link files back, reboot and see if that will relink everything rather than setting it all up one app at a time.