I'm not sure but I would make a full backup in cwm. Run the upgrade and test to see if you still have access to your apps with link2sd. If not, re-root, re-install cwm and then do an advanced restore, and restore your userdata. If it doesn't, all you need to do is wipe/reset and then restore the full backup of your v6 data.
I haven't used link2sd in a few months. I'm not sure if it can be restored that way, but it's worth a shot.