Fallout 4: NMM Plug in De-Activation - Question about Plug In Load Order

[Desie]

So I am having that issue where the mere opening of NMM will corrupt my Fallout 4 game stating that a feature (mod) is not present in the save. I have been playing happily now with all mods initiated until last night when I again decided to test my theory that NMM was messing up my mods.

They are.

I know it's a common problem and there are solutions, but this is just a premise for the following question which is about the plug in load order.

If I'm not mistaken something in the process unselects all the plug ins.

I wanted to know if it was ok to just tick the boxes in consecutive order. I know that wouldn't make sense if you have "Main Mod" and then "Sub of Main Mod". Obviously the load order would suggest you load the "Main Mod" first.

What I have been doing is just going down the 100 or so list of my mods deactivating them, signing into the game with the corrupt save. Saving the game without activated mods. Closing the game, getting back on NMM and activating my mods back and hoping to not ever have to open NMM ever again until I decide I want a new mod.

Is there a less insane way of going about this?

I will continue to search and read about it. I appreciate your patience!