I upgraded my harrowed Qullim's to tier 3 enhancement but neither of the perks became enhanced. When I upgraded my harrowed Zaouli's Bane to tier 3, it got enhanced perks like normal. It might be related to where the item dropped from, I got the Zaouli's as a random drop from pantheon and the Qullim's was from claiming a triumph. The Zaouli's also had additional perks available, idk if that has anything to do with it