Hello,
I just ran into the bug where the hexagonal amulet needed to unlock the church barrier doesn't exist - it's been a few days since I did the battle where I should have gotten the item, so I'm not completely sure if I ever got it. It might have gotten lost when I transferred a lot of my stuff to the Homestead boxes, I'm missing a lot of things there. I might even have sold it, since I didn't know I'd need it later (is it marked as unsellable?).
Anyway, since there doesn't seem to be a way to progress with the main quest, I started a new game. I noticed that my items still have the "transfer to Homestead" option even though I haven't unlocked the Homestead yet, let alone the boxes. For experimental purposes I've transferred a book and will see if it appears.
My journal also doesn't start with Day 1, but instead with the date I stopped the first playthrough.