I am setting up a new modlist, and testing as I go along. Last mod I installed was The Great City of Winterhold (which is great BTW) but when running around it, I noticed a few naked NPCs.
Then I coc to Whiterun, to do more testing and Aela, Farkas and Ria were fighting the Giant on the farm with nothing on, and no weapons (they were fighting unarmed!)
I opened Aela on SSEDIT and she has no issues - otft record, inventory with weapons all seem in order. Wondering what is causing this and how I can fix it.
Is it a bad sign if the Base and the Ref are referring to different ESPs?
Edit 2: I worked it out. I had the first version of this mod - https://www.nexusmods.com/skyrimspecialedition/mods/109152. It was applying to NPCs, and they were naked because they were too low level for their gear. Because it is all script injected, it wasn't clear that there were any issues when looking at SSEEdit. The dangers of runtime-patching, manifest!
So they DO have items in their inventory, just not equipping it. Not just armour, weapons also. I thought it could be AI overhaul, so I ran the synthesis Patcher as a test, and that didn't fix it.
Start a new game and check if the equipment is right. If it is, you most likely changed object IDs by swapping mods or replaced a still running AI script
I've encountered a similar thing before. Your situation might be different, but the culprit on my end was actually SPID, or, more specifically, multiple SPID inis distributing outfits to the same NPCs.
Skyrim can't have more than one outfit for an NPC, so if something, for example SPID, distributes two to the NPC, things get funky and the NPC refuses to equip anything. Have a look through your SPID inis for ones that are distributing outfit records, see if that's causing it