Right. Moving foward, you'll want to make new references persistent.
If this is positively the case, and I have not yet checked the new GECK update, but,
Unless the intent is to make mods that create exterior areas be expected to exist in .esm form and not .esp - - it seems best for the workflow to have the GECK automatically make objects being added to exterior cells in .esp files be persistant refs. Right now, for every piece you add, you have to click a checkbox in the item's edit window. Also, I have not seen a batch function for setting objects as persistant.
Also - - - there's the bright-white-skin-on-NPCs issue. It seems related. Unless adding new NPCs will be expected to only happen in .esm mods and not .esps, that's gonna wanna be looked at.