Okay, here's a weird one.
Last night, I cleared out all the encounters to the north of Cyseal. Mid-way through, at about level 2, I made a quicksave by the scared soldiers. I continued on, clearing out all the encounters and buildings, made it up to about level 5, and then I made a new save using the escape > Save menu.
When I loaded it up though, most of my progress was gone. My location was my the soldiers, and I was all the way back at level 2. Not only that, but my ranger's Oak Flat Bow that she had gotten before the quicksave was gone. (I did find it back at where I originally picked it up, though).
I also have lost the button to access to the Shelter Plane, but I do retain the teleporter pyramids.
I checked and the screenshot for the glitchy save does show where I was when I made it.