Anyways, the "master" mod is an .esp, and in order to add it its custom cells on a separate plugin, I turned aethernautics.esp into aethernautics.esm originally. However, as the my mod is mostly complete now, I want my mod to rely on the existing aethernautics.esp, so I used Wrye Bash to change its master from aethernautics.esm to aethernautics.esp. What I find now, though, is that every change that I made to the custom cells created in Trainwiz's mod are still the way they were before I edited them in my mod. That is to say, if I changed an object created in Trainwiz's custom cells, my change to the object is there, but so is a duplicate of the object from before I changed it.
However, when I load up my mod in the CK and set it as the active file, I cannot see the extra pieces that exist from the original mod - I only see them in-game, so I can't edit them. I also can't just delete them from the original mod, because that would require everyone who uses my extension mod to download a custom version of the original mod.
What I want to know is how I can leave the dependance of my mod on aethernautics.esp (the original mod) while making it recognize the changes to its cells that I made in my mod.
I thought about just loading my mod and the original mod and re-saving it as a new .esp file, but that would just cause the same problems that made me esmify aethernautics.esp in the first place: all my edits were created in duplicates of the cells I changed, and I would go through the same vicious cycle again without getting anywhere. Thanks in advance for any help!