While creating my first mod for Skyrim, I was having a hard time finding the weapon rack and mannequin objects in the Creation Kit, so I went to one of the houses to create copies and just bring them over. While in Vlindrel Hall I moved one of them by accident. I remember from modding Morrowind that a single change, even if undone, will edit a cell permanently unless you deleted the references with an outside tool. How can I remove the dirty references from my mod, can it be done inside the Creation kit? The only cell it changes is the Cistern.

Currently, I know of no safe external tool, so I would use the "Details" option. In the CK, go to the File | Data which brings up the list of plugin files. Next to the "Set as Active File" button is the "Details..." button. Click that. Scan through the list of records and "Delete" (which marks as Ignore) the record(s) you don't want.

What I've done when that doesn't work (sometimes it creates more problems as it's not so intuitive to know what you're actually deleting), I just load my plugin without setting it as active and duplicate my whole cell and save to a new plugin. As any change made will be saved in the active plugin, I get a copy of my mod minus changes I don't want. (I do this when I start my mod to remove the "dirty" edit from the AAAMarker cell duplication.)

One of those options will definately work.

And finally, here's a resource you might like:

Modders Resource-Weapon Racks-Bookshelves-Plaques-Mannequins by Eldiabs
http://skyrim.nexusmods.com/mods/11618#content

That fixed it! Thank you! And that file is amazing! After trying to get them to work for an hour I almost gave up any plans of adding plaques. I'll be able to release the first part of the mod very soon.

Good to hear!

If you want some other resource mods, take a look at the links I posted in this thread: http://www.gamesas.com/index.php?showtopic=1400380 The General Store has some great meshes and overall it's very easy to use and players love having all their inventory linked. I don't like that part myself, but I really love the custom activators (ie meshes & textures).

Ok, so contrary to first impression, the first option did not work. There are still dirty references in my mod.
I am concerned about doing the second one, duplicating the cell and deleting it because of the cell. I am dealing with the Cistern. I am afraid that might screw up or break the quests. Is it perfectly safe to do this?

EDIT: Not safe to just duplicate the cell. Changing the refs broke the TG questline and edited all the cells related to said questline. And somehow I have refs in Cidna Mine and Dragonsreach. this is annoying to say the least.

NO! Definately not.

I'm saying edit YOUR changes and only your changes.

Understand, any change you make is going to cause the edit flag. The idea is the edit (duplicating causes the edit, which is what caused your "dirty" edit in the first place), your changes so only those changes will be saved in the new ESP file.