wow!...so, I was standing at the door close to the lake at "the darkest hour". The door, along with the crate I had disappeared in the dark, just gone. I followed the mountain wall towards the mine. There is a place right up against the wall that looks like a texture glitch, like a piece of terrain is missing. I walked in to it, fell through the world -or so I thought- and landed at the alter in the church!! :O
I don't know how the upgrading works, can't find it out either, I literally pressed every button while hammering.
And yes, there is a piece of terrain missing there, I'm going to make an update video soon on all the glitches, problems and texture/terrain fails. Because I found something in the church, some thing(s) in the area's that are currently unaccessable. I will inculde them but since they are not supposed to be open yet it doesn't really matter. there are quite some visual glitches possible that need fixing though.
I just hope that Dasius will actually see it...