I need some more guidance. I'm going to give the whole story so all the information is presented.

I'm trying to edit and fix Jaggarsfeld, a player's home mod. The author has given the okay for mods that extend or fix it, as long as the main mod is a master. So I start off by loading the main mod up in TES5Edit and copy the USKP changes into a new plugin call 'Jaggarsfeld Extended' (this will be the addon plugin to the main mod and we'll use JE for short). After this, I add Jaggarsfeld as a master to the new plugin and save and exit.

Next I load the new plugin in the CK as the active file. The exterior navmesh is the first thing I want to fix so I delete all of it to start from scratch and save the file. At this point I just want to check to see if the changes are being retained. So I load the files in TES5Edit again because I know I'll have to re-add the main mod as a master to be able to work and save the changes in the CK to the new plugin (unless I'm doing this wrong). I noticed the new navmesh data for JE is present so I re-add Jaggarsfeld as a master again.

Next, I load JE in the CK again to start work on the exterior navmesh. I noticed that the CK duplicated the mod's worldspace which is fine since I'm not saving to the main file and saving to JE. However, this is where my issue lays. When I load up the Jaggarsfeld worldspace (HunterCabin) and go to edit the navmesh, the main mod's navmeshes are shown rather than my the saved JE navmesh, which are currently empty since I deleted them. This kind of makes sense if the CK is saving the information to the duplicated worldspace. The question is, how am I suppose to get the navmesh from JE to take priority and work with them rather than ones from the main mods? I suppose if this is saved in the duplicated worldspace there would be no way of doing this.

The only way I can think of getting around this is by completely duplicating Jaggarsfeld's worldspaces and saving them to JE. Then I would only work from those duplicated spaces. This would be okay, however, I'm not sure how this will effect things down the line. I suppose I might be able to load JE in TES5Edit, re-add Jaggarsfeld as a master, and then clean out everything that is "identical to master". This, in my head, sounds like it would create a plugin that only adds or replaces things from the master, Jaggarsfeld (main mod). However, I don't think TES5Edit cared for the duplicated space.

It might be better to do all the changes to the main mod, then rename it when done, add the main mod as a master, clean it, and then call it a day. Is this the proper way to make an addon to a mod that adds, fixes, and removes things from the main file?