First off - this is NOT an issue with TES5Edit. It's an error in my mod.

I used Check for Errors to check the .esp, and I get this:

http://pastebin.com/uK9nqwBp

Does anyone know the source of these errors? These fragment scripts once referenced global properties, but I've removed that from the script fragments (open in external editor, delete Papyrus property, compile). They now use (GetOwningQuest() as MyQuestScript).MyVar instead. I've verified the scripts show no properties with the edit property button, and have no properties or references to them in them.

Did you clear the properties via the edit properties window before you removed them from the fragment script code? If they were not cleared and saved before you removed their declaration in the script then you have introduced dirty edits. I wouldn't be surprised if your papyrus log throws up lots of complaints about it.

IIRC what you will need to do is re-introduce / declare (just declare nothing more) them in your scripts, fill them in the edit properties, save, clear them in the edit properties, save, and then finally remove them from your code..........Hope I got that right.

Don't know if there is a way to do this in TES5EDIT?