I have the current Mod set up: a Master containing a lot of Spells, Abilities, and background Scripts; and a .esp that contains more Scripts, Items and Abilities-- plus two edited Cells. What I was wondering was, is there an easy way to quickly and accurately transfer everything except the edited Cell-data into the Master? Right now, the Edited Cells contain roughly 25 items that are referenced in Scripts-- what I'm planning to do is comment their references out, and then un-comment them in the modified version.
I'm pretty sure TES4Edit can do this, but I'm not confident enough with the Program to try it myself, so was hoping someone could give me a step-by-step guide, if possible.

I'm not sure if it works but:

• Convert your esm to an esp with TES4Gecko.
  
• Merge the created esp(which was the esm) and your real esp with TES4Gecko.
  
• Convert the merged esp(contains everything from both esps) to an esm.
  
• Finished. You should have now an esm containing everything you made.

With TES4Edit, tick the ESM flag in the file header (hit F2 while mousing over the empty space to the right of "Record Flags"), close, save, change file extension and all will be right. That's probably exactly what the Gecko does, but I tend to stick with TES4Edit. You can also ESM'ify with the CS/GECK by changing the file extension to ESM, opening, then saving the plugin. The editor might crash afterward over its active file being a bona fide ESM, but it'll assuredly tick the flag.

Afterthought: You could (since they're already persistent) add those 25 references to a new and otherwise empty cell in your ESM and use http://cs.elderscrolls.com/constwiki/index.php/MoveTo to place and position them in [00] cells, alleviating the need for an override esp as well as the oddities which occur when an ESM overrides another ESM's CELL and/or WRLD groups. Too bad Oblivion didn't have Fallout3's ONAM list... There's always TESV.

Thanks, that's really helpful-- I thought any CELL edit would cause the Vanishing Land, but if it's only Exterior/Worldspace Cells which cause it (esp. since I'm only using these as Stores for background pieces right now-- using MoveTo already), then I can use that

One less plugin to maintain, right? The whole rug pulled out from under you thing only happens when ESM(s) placed stuff is overridden by another ESM, so a brand new cell won't incur that madness.