You can't move the linked clones in anyway to another datastore without causing problems. I just had to do this with around 100 linked clones. The only option I was aware of was to create a manual pool, shut down a linked clone, clone it to a new vm, start it, remove it from the domain, add it to the domain using the new name, and then add it to the manual pool. It was about 20 minutes of download per desktop for me over a few weeks.
