How to merge two hundred mods
From Nexus Wiki
Note: Some mods it's better to just apply a filter so that it filters out white (single entry) then the flatten trees or whatever (so cells an worldspaces are flat) Then work your way down making edits to the duplicate entries. Most of the time just making them match the master. In cells just look for obvious mistakes, an keep it if you trust the mod (later on any issues will get red flagged) Most of this is just to make sure they didn't change something that you didn't want changed. Then just clean the mod like the FO3edit guide says about removing identical to masters an setting deleted to disabled. Then merge it, then one at a time doing the same thing any major issues will get red flagged in the filter.
No way is that even possible. Bah sure it is. Fallout 3 NEXUS has a never ending amount of buildings/places mods which all are totally awesome. However, most of them overlap in the either the vanilla content in which they change or the location in the game world which they are at. The Read me should tell if it's going to conflict with another area of the game world. Then there's no way to tell if the various modders that made these awesome places changed the same things. Like a tree, one modder moves it this way, another moddder moves it that way. Now it's floating in game.
What's worse is if a modder deletes the tree, then another mod that moves it loads after it. Which will cause one of the worst crashes in the game. Now consider all the other vanilla content often edited which is a lot more complex than just a tree. What if you don't want all that fancy complex stuff like scripts or quests because you are just wanting to merge all your Buildings/places mods into one huge mega mod. So that you could use 200 of them. Maybe you just wanted the simple part of the mod, the cells. Or other reasons.
I stumbled upon an answer, because I'm currently building a 100% conflict free load order, while also merging things into Mega sized Zergs .esp's lawlz You can figure out most of how to reduce a mod down to just the cells from what the guide says about cleaning mods, which you should be doing anyway @ Link
However I've found that FO3edit is really only good for the basic cleaning as discribed in the guide. For one thing it doesn't give you a warning about the users of something when you delete it. Also it just feels risky removing Nav-mesh data with FO3edit. So if you are planing on reducing a mod down to just the cells an the things in them, and nothing else. It seems more safe to use a combo of the GECK and FO3edit. Use FO3edit to perform the basic cleaning, then open it with the GECK as a sort of pre-delete of things. You get the warning for the users on the things that have related references, can also use the special tool to remove Nav-meshes. It would be tricky to save the Nav-mesh data, because sometimes it's interlaced with the vanilla cells or wasteland in the Nav-Mesh map data you see in FO3edit. A pre-delete with GECK removing all the Door teliport markers in the various cells the mod adds (which would also let you place the mod anywhere later on) Then using FO3edit to delete the Nav-mesh map data (keeping the actual cells navmesh) then open with geck an finalize the mesh after your new door teliports are in place (which might rebuild that Nav-mesh map data we see in FO3edit)
But this isn't tested. I'd rather just rebuild the Nav-meshes myself so that I know it's right and clean. It's a lot of work yeah, but not as much work as re-building the cells, which is where the bulk of the work is done in these Buildings/places mods. You would lose any of the good content though, but you wouldn't have to reduce a 100% clean mod. If it's clean just merge it as it is. The mods which change either vanilla cells or the wasteland, would need to be reduced though for obvious reasons.
Now an example...
I pretty much get a mod almost 100% conflict free in my load order before I merge it. Which at that time I'm also checking that there are no duplicate entries between the mods I'm about to merge together. This worked great at first I got 5 mods ready to merge, but had problems with the 6th. The first 5 were all pretty simple an clean, just adding new cells. The 6th was huge and also complex. Scripts and quests, and a bunch of fancy stuff. Also vanilla creatures were duplicated which broke MMM. Then some of the vanilla items were duplicated an therefore changed. :( Then the thing had 35,000 duplicate to master entries, with about 5000 hidden by moving the items a few units or even 0.0003 of a unit.
Needless to say it was pretty obvious that creating a merged mod of 200 buildings/places would be impossible. After about a week of failures an having to start over from scratch with the backup copy of the .esp for this dirty mod I figured it out. Basicly I'll clean it following the web-ensized FO3edit guide, then change the name of something simple like an armor (this sets the mod so that it needs saving) Switch the name back, then save it. While I'm also looking at the mod for what it is I need to remove. Next I'll open it with GECK. In this example I'm just trying to save all the hard work which was done in order to create the cells. So I'll start by removing the door teliport markers in the GECK for all the new cells. I'll save that, then start deleting things I saw while viewing in FO3edit which I thought would be a problem. So that the warning will pop up on the other users of what I'm deleting (because that stuff would have to be changed) Which I'll either make the changes on the fly, or write them down an change it in FO3edit so that this item doesn't use that script or this marker which is part of a quest an such.
Really all you need to have done in geck is the Door teleport markers, or the whole Nav-mesh if you want to be safe. (like I said removing actual Nav-mesh data inside cells with FO3edit is kind of scary) At any rate anything you delete in FO3edit which has another reference using it will show up as  Error could not be resolved, so really you just look for that stuff an delete it as well. Like placed items in cells, say I delete the creatures the mod contains, well in cells where ever there was a placed creature it's going to Error (which these Errors seem benign at least) However all you do is click on the name tab so that it will now sort the list in either A-Z or Z-A an the Errors will all stack up at the top or bottom, making them easy to find.
There's no way to really know if what you are deleting will cause a problem. Which is where the GECK comes in, just find the other users for that item an fix them. Mostly my plan is to just delete everything, an remake the Nav-meshes, because I want to make sure it's 100% clean. Any Advanced content I wanted to keep I'll either keep it in there or add it back in later on once it's merged.
The other bonus is since you are going back into the mod with it set to active in order to remake the Nav-mesh or keep the Nav-mesh an only move where the doors to the cells connect to the actual wasteland (so that tons of more mods can be used togehter) You can also set this mod to use FOOK2 as a master or 20thcenturyweapons any other mod which would allow you to place tons of cool loot in these really cool cells.
I have this dirty mod cleaned up now, so I'll merge it in, then work on it. Which before merging it might make a good point to rename the cells so that they all stay together in the list (for future reference) Say the first dirty mod I merge with a clean unchanged mod. I'll rename all the cells to
zzzAaMyBase134 zzzAbMyBase134Bathroom zzzAcMyBase134Armory zzzAdMybase134Sewer
The zzz can be AAA if you wanted, it just puts the cells at the very top or very bottom, then the next two letters keep the mods seperated into groups of projects. Like the next dirty mod would be Ba Bb Bc Bd an so forth, so later on I can add an fix stuff because I know where to look.
zzzAaMyBase134 zzzAbMyBase134Bathroom zzzAcMyBase134Armory zzzAdMybase134Sewer zzzBaVault125 zzzBbVault125Entrance zzzBcVault125Armory zzzCaPornStarHideout zzzCbPornStarHeathDepartment zzzDaSuperDuperVault zzzDbSuperDuperVault2 zzzDcSuperDuperVault3
One time thru no fault of their own, a modder added duplicate entries for reflection/refraction data on all the items in a few cells. Two added refraction data entries for each item, with a total item count of 300-800 for each cell. In this mod there were tons of duplicate entries which was just from the clicking an clacking of creating things in the GECK an moving around from cell to cell. Basic cleaning won't get rid of this extra data, so you have to keep an eye out. Also it doesn't hurt to have a unchanged backup, or backup in stages durring your reduction/cleaning. A lot of the time you have to start over because it's not our job to fix these mods because we know nothing about them, that's up to the mods creator. But trial an error is the only way you can fix it yourself, so make backups an save before you do something you don't understand.