Not as easy as Fallout 4 merging it seems. I tried to merge a bunch of cut content mods, and then later on I installed a mod that had a patch for one of those mods, and when I installed the patch Mod Organizer read it as missing a master file, I'm assuming because of the merged plugin.

Anyway to make it not do that and make the merged plugin work correctly?

There's no way you would get the game running when missing a master-file for an active plugin.

If I were you I would go through each entry of your merged plugin and check if the patch changes that specific record. If so I would manually adapt the enty of the merged plugin to the changes of the patch.

In case you didn't know already, there's a good manual:

Code:

http://www.nexusmods.com/newvegas/mods/38413/?

I just scrapped the entire virtual install and decided to go again more carefully. I have a feeling it wasn't starting up because of the fact I had all my Freeside Open plugins mixed in with a general cut content merged plugin, so the patch for FSO from another mod didn't have what it needed.

Everything is explained in this video:
https://www.youtube.com/watch?v=0S6cpCwTezE

I think I figured out what my problem was.

Because the plugin that the other one depended on was in the merged one, it couldn't activate.