Boolean operation destroying topology-deleting faces I am modeling a chair, and I am trying to achieve the rectangular holes in the chair by using a specially modeled boolean object for them. The holes are supposed to look somewhat like this:
Here is what my chair looks like before a boolean: 
This is after applying a difference boolean to the chair for one of the cubes, and deleting the cube:
As you can see, the boolean operation deletes faces around the hole it creates. I made the first hole by doing the same thing, but manually creating faces by pressing 'P'. I've tried CTRL+T in edit mode to triangulate the faces, but in vain. Is there any reason for this? .blend here:
I tried deleting those faces, but the result still was destroyed topology.
So, First, you have overlapping vertices. 
Select all your vertices with  A  in edit mode and vertex select mode, and Press  ALT  +  M  > by distance in order to eliminate double-vertices.

The real problem is you have 3 inside faces which mess up your boolean operation. Notice how in wireframe view, some faces have a clearer shade of grey. That means there are faces which shouldn't be there. Also note that there are some issues in the leg of the chair, but you will be able to fix them with the same technique :



In edit mode, select faces around the 3 culprits and press  H  to hide them. Then go in face select mode by pressing  3  , and select them. You have to select next to its little dot which may or may not be easily visible. Press  X  to delete, then select "only faces".



When all the culprit faces are deleted, while still in edit mode, press  ALT  +  H to unhide your geometry. Result :