Wow, that's rather unexpected. For me getting a good Church ending was the most obvious path. There are guides in this Community. I can provide a save game before going to church (something around day 4 I think), if you'd like. I play on Windows if that'll do
https://filetransfer.io/data-package/wuJ3tXk6#link
I remembered. On my first playthrough I was in no hurry to go the church. I talked to priestbot first and met the nun only on the next day. On my second playthrough I went to the church straight after MC was mentioned it. That time it is the nun who was there, and the priestbot on the next day. I talked to her and choosed the option to cheer her up (that she is capable to become a full-fledged nun). It's the first key option. Then I noticed that their place is in rubble - it's a the second key option. On the third day priestbot fell into BSOD after update, and the day after that I agreed with nun to help them - third option. After priestbot returned to normal state I convinced them that he should go to the Vatican and check for himself what happened - fourth option. The best way is to visit church on nun's hours and not before.
