Unfortunately, I don't have to much experience with terrain building, but did you rebuild the AI ?
I did that for some tests in XC_Bags and had the weirdest behaviour, less with not being able to move but with the Cyseal library upstairs being visible only partially. I gave up on AI building afterwards but as far as I remember, I could no longer go downstairs.
What I did not test was renaming MainLSF.pak but that one is the reason for so many shortcomings that it's a good candidate to look at ...
