I used Morrowind Enchanted Editor and opened some Cells and looked at the FRMR entry object indices.
The original LGNPC object indices differ from the indices in my merged mod.
So it probably can't be safely used with an in-progress LGNPC save. You have to start a new game to avoid problems. The TESCS Combine Plugins does renumber the indices.
If anyone wants me to release the merged LGNPC I have let me know and I will try to get permission.
A way to merge and play a on-going game could be
(example with 2 mods to be merged, you can see starting reference numbers of a mod in Mash\Renumber refs.)
mod A.esp, has references renumbered from 42000
mod B.esp, has references renumbered from 33000, loads after A.esp
With Mash\mods
1a. select mod A.esp, File\Duplicate as A1.esp
1b. select mod B.esp, File\Duplicate as B1.esp
2a. select mod A1.esp, Renumber Refs, input 1 (standard)
2b. select mod B1.esp, Renumber Refs, input 1 (standard)
3a. select mod A1.esp, Updaters, select A.esp
3b. select mod B1.esp, Updaters, select B.esp
With TESCS
4. load A1.esp, B1.esp, do not select active file, combine loaded plugins as A1B1.esp
With Mash\saves
5. select a recent save, File\Duplicate as testgame
6a. select testgame, select MOD A.esp, right click, Change to... A1.esp,
6b. select testgame, select MOD B.esp, right click, Change to... B1.esp, Save
7. try loading testgame in Morrowind.exe and play a lot. if it works, you could be able to safely use it also with merged A1B1.esp
From Mash\saves
8a. select testgame, select MOD A1.esp, untick it
8b. select testgame, select MOD B1.esp, right click, Change to... A1B1.esp, Save.
A lot of work, and untested, but this is what I'd try if I'd want to reset some mods to standard reference numbering (starting from 1), merge and use them on a on going game.
[EDIT]typos