Unless someone tells you from their own experience whether it does or doesn't affect the live tree, what I'd do is copy the live folder tree so somewhere else on the drive (say the root directory) and then try it. If it does delete the live tree then you can simply copy it back.

Alternatively simply manually delete the PTS tree, I know of no reason that'd break anything. The ESO client has no registry settings, DLL registrations etc. that are 'undone' when you uninstall so brute-force deleting would seem to me to pose no risk: but on the safe side I do image my disk when I try something like that.