It seems someone snuck in a malformed quest stage script for DLC1VQDragon and it FUBAR'd Durnehviir's behavior after the fight.

I deleted the offending script... however, the quest is Start Game Enable'd, so there are a lot of empty quest script vars for the affected script.

Is there any way to re-fill those variables, either through the console, or through another script? SetPQV won't avail me, because it doesn't seem to work on reference vars, only numerical or string vars.

Well, yes. It won't work for Actor or Object Reference properties (unless they're already persistent...?), but you can make a dummy quest with properties mirroring the borked ones and do:

(Quest as QuestScript).Property = ExternalProperty

and do that for every broken property.

You can technically do it for a QF, but you need the script name down exactly.

Reset the quest w/o the script overridden? You might have to untick its "Run Once" flag so all of its vars/properties will properly revert.