My mod was working perfectly fine last I play tested it but now the meshes do not appear in game and the custom sounds do not play, yet they appear just fine in the Geck and the scripts I made still work. I haven't added any new mods and my save games haven't changed, the only thing that has changed is that I added Mothership Zeta to my esp so I could use the cryo effect on my new scripted weapons, so anyone how I can resolve this without removing the Zeta esm from my mod?

P.S. The mod I'm making is adding weapons that can change ammo types from normal to poison, inferno, cryo and disruptor (just the same kinds of weapons just with different effects witch are swapped using the script) all this is based on Mass Effect's Ammo types.

HOW did you add the Zeta DLC to your esp? Did you just make use of the zeta effects in your mod, or did you try doing it using FO3Edit? You should only have to assign a use of the DLC content in your esp and it will include the DLC as a master automatically. Mod load order shouldn't affect things already in game or called by script, so I dunno.

yes thats what I meant I added/assigned it as a master I didn't merge them (I don't think thats even possible, not without a crap load of work)

Nevermind I found the problem. Fallout 3 unlike Morrowind uses 2 different weapon models the world model and the 1st person model, I modified and renamed the weapon mesh and forgot to reassign it to the 1st person static, now that I've done that its working again. I really need to unlearn or forget morrowind while using the Geck as I keep making simple mistakes like these cause of it.

What I meant was loading zeta and your esp (as active), at the same time. Then when creating your weapon or whatever it is you were doing, just use the loaded cryo effect just like if it were a default fallout effect. It creates a link to the zeta effect, and adds zeta as a master automatically when you save your esp. No merging whatsoever and no dinking around with FO3Edit either.
Anyway, good to hear you sorted it out.