I know I can mod my house that's not in the city (I do it all the time), but now I'm trying to mod my mod house in the city. I have house mods for all of my houses in the city,(the ones you get once you become Thane in a city). Example: I'm trying to mod my modded Hjerim house. I go in to the CK and select it when I load the data, I make sure that box is checked in front of the mod to make it active. But it wont show up anywhere else once the data loads. I can see the original generic Hjerim house. But my mod Hjerim house wont show up anywhere to select it and have it appear in the window so I can make some changes to it. Am I doing something wrong or isn't it possible to mod a mod house in the city that replaces the original house?

Putting an X in front of the plugins name does not make it active. You have to click the button 'Set as Active File' as well. The Status will then change from 'Plugin File' to 'Active File'.

I've done it that way too, it still doesn't show up.