Renaming rather than deleting is just a convenience, in case you want it back. It wouldn't function any differently.

The idea is that if you have windows that were placed while the CEP fix was in place, they are the ones where the windows are repositoried to the doors, so they need the doors to show their recolors. If you have windows that were placed without the CEP in place (like when I made my hobby lots the first time, for example), then they show recolors fine, but they are not repositoried to the doors so in a game where color depends on the doors, they will reset to red, the default for the doors. In a game where there is no CEP, they will show recolors and be recolorable and keep their color, there is just no connection to the door.

Maybe your game has a combination of these or something that is making it confusing. You might want to check in a clean game folder. I would expect that you can choose to have the CEP fix or not, and then delete and replace all affected windows to match which ever you do. Also be sure you do not have the FatD fix as well because it does the same thing as the CEP. Recolors of the window that are made with the CEP may also confuse things. I didn't have any to test, but it seemed like they might.

If you use the CEP, you want the CEP Extra.

The CEP repo's the windows to the doors, the extra fixes what was broke when the windows were included in a later EP. (no idea why the CEP wasn't just amended?)