Ok, well I am editing a town in the CS and somehow two cells within the towns world space are now missing. Within the CS everything looks normal, but when I load the plug-in the ground is gone. I do not even know how to delete a world space cell, so I don't know how it got deleted. If I go over to the groundless cell in game, I can look down and at the very bottom is water, this led me to believe the water height may have been altered but I check that and raised it but the ground was still gone. If I fall down the cell I end up in water, but if I swim to the end of the water, I am put back on the normal ground. So, I tried to covered it with fake ground but no objects appear in game. I also tried to go into the details of the plug-in and delete any changes within the cell, but I could find nothing. Well I hope someone can help me because I am dumbfounded.

Do any of these cells contain extremely steep terrain in the CS? Is this worldspace vanilla, contained in a .esp other than the one loaded as active, or contained in a .esm other than Oblivion.esm? Do you get any error messages when you load or save the mod? Have you tried adjusting the terrain slightly in these cells and saving to see if the error is fixed or if you get some message upon saving?

Both of the cells are flat. The world space is not vanilla, it was a mod I downloaded and am now editing. it was fine until I started deleting objects from the cells and i must of done something to them. it does have an esm but only the esp has been effected, and it is the one that is active. I do not get any error messages, and I have tries changing the terrain several times with no success.

Do these cells have trees, bushes, or other vwd objects by chance?

Does the .esm contain the landscape for this town, or is this town entirely within the .esp?

Am I right in this by assuming that:
Oblivion.esm
.esm
.esp (active)
is what you're loading up in the CS, as opposed to
Oblivion.esm
.esm
your.esp (active)
or
Oblivion.esm
.esm
.esp
your.esp (active)
or something like that?

Well, originally, they did have trees and bushes but I deleted them, But I think one of the trees is still there, that I deleted from the CS but it still appears in game. the .esm does contain the landscape

Oblivion.esm
.esm
.esp (active)
I am editing the original esp that I downloaded, I didn't start my own and add it on.

It happens because the game has trouble registering vwd for objects in cells which are part of a .esm which is not in the 01 index. Either you need to delete the objects completely and replace them with new objects which only exist in the .esp, load the .esm in the 01 index, or remove the vwd flag from those objects with TES4Edit. Changing your load order to place the .esm immediately after Oblivion.esm when playing the game should confirm this.