Pointfile leaks after mirroring my map

[KubeDawg]

So today I finished my base. It is complete. So I saved it under a new name so I'd have a backup of it and proceeded to mirror the base.

First, I deleted the skybox at the front of the base, then went to map properties so the entire map would be highlighted. After that, I shift-dragged the base over to a good spot, hit Ctrl + M to rotate it on the Z axis 180 degrees, then lined it up with the other side of the base. Finally, I stretched the skybox/ground to connect the two bases. Verified no leaks were visible and every time I compile the map, I get leaks. I load the pointfile and it takes me to a brush until I replace it with a new one. Then it moves onto another one and so on and so forth until I just got fed up with replacing the brushes.

So I save and exit the map and when I pull it up again in hammer, the mirrored side I just created is completely gone with the exception to those brushes I replaced manually. Am I just doing this wrong or am I going to have to remake the base from hand on the opposite side?

I also tried a different method to mirror the map using Ctrl + L and Ctrl + I but that got a similar result.