Pardon me for asking, but noticing your post count, and seeing that you're posting in the CK forum, I'm not being egged on here, am I?

In any case; before starting the CK, rename the .pex that's giving you problems, find the source file for it in the source folder, and make a copy of it somewhere. Enter the CK and load up your mod. Go to where the offending script is attached (activator, etc.), Right-click on the script and select Edit Source. At this point, what you might want to try is removing or commenting out all the script in the source, leaving only the name at the top, and press Ctrl-S to save and compile it. That should get you a .pex with no code or properties in it, essentially a blank slate. Save your mod and you should be good to go. I'd run it and make a save at this point, then load up the mod in the CK and uncomment the code and properties, removing any that no longer refer to anything valid in your mod.
I'm thinking this should get you going.
-HB