I'm having an issue where I create a new .esp dependent upon another in TES5Edit by deep copying as an override an entire section of forms, such as weapons and armor. I'm

? opening up the new .esp files in the CK, creating a new leveled list using those objects (which are easily found since they contain an asterisk in the count field)
? add the leveled list to an existing one for later bashing
? saving the file then opening in TES5Edit again

Suddenly, on some files, the master dependency has been removed and the form IDs for the overriding weapons and armor have had their first two decimals changed. This results in missing things like 1st person weapon models and so forth. Anyone have any ideas what's happening here?

Apparently the problem is that the CK strips .esp masters. The solution seems to be opening up Wrye Bash and re-adding the original mod as a master through the right-click menu, then everything looks normal in TES5Edit.