The collision of Luigi's mansion is completely separate from the furniture itself. So yes if you delete furniture entries for a specific room the collision for it will be there still.

To get rid of it you need to edit the collision itself which is located in the map file ,but if your just editing the mansion then you edit map2.szp.

I will make a step program for you to teach you how to edit collision.

Step 1

Download Collidah from here

Step 2

Extract the Collidah folder and put your map2.szp in it and put this cmd prompt in there too

Download Cmd.exe from here

Step 3 

open the cmd that you just put in the Collidah folder and type the command "Collidah map2.szp" to export the collision. The collision will now be converted as an obj.

Step 4

Download the Blender program from the website and install it. After that is done open the obj in Blender. It should look something like this. also make sure to put the view end to 50000 in both edit and object mode to be able to see the mansions collision.

Step 5

This is where things get nasty the mansion is comprised of a bunch of weird meshes so you will have to select them all

Step 6

Go into the modeling tab or edit mode and then switch from vert and face select to remove the furniture collision or any collision you desire, but you must know which room it is in. 

You can also add collision if you want but you must use one of these materials for it to work in game

The materials determine what sound is played for the foot steps and the ice material makes it slippery for you.

Step 7

 Once your done removing your desired collision you can export it as an obj over your old collision.            MAKE SURE YOU CHECK TRIANGLATE FACES ON THE EXPORT. It could break it if you don't.

Now if you want to place new collision you need to grab the cords from the furniture you placed.

Note: In blender the y and z collision positions are swapped. so your z will become y and your y will become z. Also the if the z position was negative in your coords then it will be a positive y in blender and the other way around. this does not apply for the y position in your coords it will remain the same.

Step 8

Now run the cmd again and this time type in "collidah col.obj map2.szp" and then you should have your new map with its new collision ready and then test in game.

Note: make sure to backup your original exported col.obj in case something goes wrong. also make sure the normals are right before exporting and make sure everything is flat shaded.