According to a growing number of bug-hunters in the Fallout 4 community, such as Velderin, Arthmoor and Sclerocephalus, a recent patch from Bethesda has broken how settlements - a core part of gameplay - work.
...it's been optimized to reload settlers from a list instead of saving them for you. So imagine that you sort out your settlers and turn around for a second and turn back, suddenly they can have a change of appearance, but also reload all of their gear as well as reset them for work... [a]pparently any mod touching workshops (or possibly even just scripts at all) can break settlers. Or even just vanilla (most likely more on consoles with the patch hitting hard to free resources for the game).
It seems that in order to reduce overall memory requirements, settlers "not in view" are being unloaded from the game entirely. When the engine reloads them, it's from the same scripts which create new settlers. Anything about them - appearance, gear or jobs - is overwritten in the process. If you just spent five hours collecting combat armor and shotguns for your settlement's guards, kiss all that goodbye.
Ironically, it was a mod which brought the issue to light by making Fallout 4 run much more efficiently with lower memory loads: Arthmoor's Unofficial Fallout 4 Patch. Because scripts processed faster, the engine began unloading and reloading settlers more frequently than it normally would. Turning away from a settler could potentially produce a reset, even if you turned back only a few seconds later.
While any mods affecting settlements will accelerate the rate at which this occurs, it can purportedly happen without them. Even official DLCs, such as Contraptions and Wasteland Workshop, may also contribute. Provisioners and quest-related NPCs such as Preston Garvey are immune, since the engine keeps permanent records for them. Per Sclerocephalus, who's been doing a lot of heavy lifting in the bug-hunting department:
I'm running Fallout4 with no settler mods, no settlement object limit uncapper and no mods to add new items to be constructed. I also have the Workshop DLCs (Wasteland Workshops and Contractions) disabled. In addition, I'm running all settlements with low settler numbers (five)... I have the Unofficial Patch installed though. With this setup, I have not seen the issue occurring.
He's also, after twenty real-time hours of debugging, put together a more detailed report. The TL;DR? The Workshop script, central to how settlements process functions, doesn't play well with modifications of any kind. That includes just recompiling it, without any changes at all. A new version of the Unofficial Fallout 4 Patch has been pushed out as of yesterday, which appears to incorporate Sclerocephalus' fixes.
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