This happened to me as well. I’ve tried everything except deleting the altar and rebuilding. It’s kind of annoying too because Set priests look the best and can’t even see it because it’s stuck inside the altar.
Don’t rebuild the shrine
I finally dismantled my altar last night and rebuilt it on flat ground in a different spot. T1 is good but upgrading to T2, priest still stands inside it
I removed him until it had upgraded this time because on the last shrine I had just let him stay on the shrine during upgrade. Tried removing him several times after upgrade and putting him back but he just seems to prefer standing inside it.