You can safely install the latest patch and keep playing with your existing saves.
Do you mean the door that was locked by one of 2 guards when you entered the room? If so, you will not be able to open that door until later. Jump down the pit in the arena, and continue exploring.
It is a known issue that the BF fog-of-war sometimes gets reset. If you keep running around, it should clear again in largish blocks.
BF quest items and monsters are placed randomly on the third levels of the dungeons, so it is possible for any particular dungeon to have none, one or multiple items or boss monsters.
Is the entrance to the next dungeon level in one of the rooms you can not get to?
Sometimes an entrance can be partly or completely obscured by a wall. Check the auto map, to see if you can see some blue sticking out somewhere. Running around methodically searching with the mouse can also help.
Occasionally the entrance can be a pile of rocks, rather than the usual fountain thingy.
Rarely part of a level can be separated from the rest, which could contain the entrance to the next level. Since there are a couple rooms you can not get to, that may be the case here.
If you click and hold the mouse button down to direct a character, does that work any better than just clicking past the door?
Alt-tabbing out of the game and back can shift character positions slightly, so if you get both characters as close as you can to the door (or a wall) you may be able to alt-tab repeatedly to get them through. Doing this with other NPCs around can cause problems if they get through a wall and become inaccessible.Teleporting anywhere (via hex editor)
Alternately, you can just skip the rest of that dungeon. You may miss one or more BF quest solutions by not getting to the third level, but completing the BF dungeons is not necessary.