Recently I've done so more work with my mod Blackreach Railroad. One of the things is does is modify certain dwarven ruins to have an extra corridor leading down to the train stations. These portions remove existing caps or corridor pieces and change them around so the player may access the new corridors.
In game, the portions I removed are still there, blocking your way. In the creation kit however, they are not.
So what's the problem?

You probably just have a buggy save. Start a new game or load a save before the mod was installed then see if it's there.

I did, the walls are there regardless.

are you deleting the walls from the vanilla game?

if so, it's not a good idea, and your problem is one of the reasons why.

it's better to move the wall out of the way somewhere in the void rather than deleting it

I checked. The walls are moved out of the way, yet they aren't in game.