Not sure why you want to use junction here, what not symlinks? Nobody with xp/2000 or 32bit is going to be doing this.

I think your better off having two wows, one for patching and one for running in the hybrid ssd+ramdisk.

Have the startup for the hybrid maintain the data directory; create the ramdisk, format it, and mount it. When you would mount it not as a drive letter but just as your data directory. Then you can robo copy over the patched data directory contents. If you wish you can mount both as a path and as letter.

I can imagine making a volume clone on disk to restore this faster than the copy.