You won't believe this.
I made an awesome fully upgraded rifle all from salvaged parts from other maxed found weapons (need max out perks, I meet only half the requirements), so yea, that project took a lot of time to do.
So I mod this rifle, pour my love into making it, put some thought in naming it, then store it in shared workbench for later use (it automatic rifle so I decided to hoard 2000 rounds before using it).
Then some in-game weeks later I check the workbench stash and my rifle is gone! AND AMMO TOO! WHAT THE...!!!
I then remembered that this settlement suffered 1 attack in its whole history and that we defended it, so I figured that the attackers ran off with my rifle! But then my gut told me to check
the settlers and see if one of them "borrowed" my rifle. AND I FOUND HIM! Blasted thief took the rifle, dropped all mods from it (it was now completely unmodded), and also took 1534 ammo!
I probably don't have to tell you what great pleasure I took in delivering some sweet, sweet wasteland justice to THAT BASTARD. And then I built a fence around my workshops. svck ON THAT, SETTLERS!
BEWARE OF THE BLASTED THIEVING SETTLERS!