To convert the rest of the game to 3D it required re centering a lot of maps... Meaning, where you were standing in old saves may now be inside of a wall..
BUT! It's an easy fix, go to MENU and teleport back to town. It will fix it, and this will never both you again. ENJOY THE 3D ENVIRONMENTS!
Converted rest of game to 3D.. But
Source: Steam Community (opens in a new tab)