I've tested this and it works but I wanted to make sure there wasn't a reason I should avoid doing it since I saw no official way of changing the replica location of a linked clone other than recomposing. We are on View 5.1 currently.
I had a pool of persistent desktops that were initially NOT set with the "Select separate datastores for replica and OS disk."
Since this occurred when we just started using the system we didn't understand that meant a replica would be created for every datastore it put one of the VMs from the pool on.
Now I've set the setting in the pool to select separate datastores, but I see it does not affect linked-clones already created.
So I modified the two .VMDK files (<VMname>.vmdk and <VMname>-digest.vmdk) that contain the "parentFileNameHint=" property on one of the VMs in the pool and successfully got it to use the replica located on the datastore I wanted them all pointing to.
So what I plan on doing is manually going through all the linked clones and point them to the single replica on the single datastore I want using that same method.
I've seen no ill effects from this. I tried refreshing the desktop and it worked fine and continued pointing to the right replica.
Does anybody know of a good reason to not do this?
Thanks!