Modding is a big part of gaming right now, mostly on PC although a few games on the consoles are getting the same treatment now. However, it's worth remembering that these mods are fan-made and so sometimes... don't work quite as intended.
The Fallout 4 Unofficial Patch was released to fix a batch of smaller bugs that Bethesda overlooked, much in the same vein as their previous Bethesda game patches. Only this time, something's begun to mess it all up and that thing is Settlements - the very thing that Fallout 4 pushes as a central game mechanic.
Detailed extensively on this forum post here, the issue is that modded scripts seem to be making the game reload NPCs regularly. This includes your settlers and anything that the game isn't told to remember is randomised each time they're reloaded. Unfortunately this includes such things as the settler's held gear, appearance, gender and even the species of the settler. Also, the reloading can happen even if the settler is just out of line of sight. So turning your back on your settler's designated guard could have them turn into someone completely different when you turn back to them and their specially modded weapon could be replaced by something basic as hell. Oh, and it also stops new settlers from being recruited at all. As I said earlier the settlement mechanic is central to the game so if you enjoy that aspect of it, this isn't good news.
They think it has something to do with the scripts that edit specific files relating to the workshop, but a Bethesda employee spoke up on the topic to say that they don't agree. SmkViper has denied that it is the fault of the scripts mentioned, as well as saying the mod makers' misconceptions about how the coding works could have them barking up the wrong tree. Regardless of this though Bethesda seems to be working to replicate the bug to see how they can help resolve this. For now, a temporary fix is in place with the mod team having removed part of an AI routine. Unfortunately those settlers who changed during the bug will not be able to change back.