There appears to be some sort of bug in the way object transition to and from containers happen. Either something isn't getting transcribed or something is getting borked in the persistence, but I've had it happened and others in my company have too. It's getting more and more common (possibly related to the performance updates)
Shortly after this happens, some GC process seems to eventually clean it up and the item is fully destroyed, but it honestly means that ANY piece of gear in the game made from a blueprint could spontaneously poof into nothing.
This has a chance to happen when an object is put into a container, taken out of a container, or when you remove it from your equipped items. It's... REALLY annoying to lose sometimes very nice items that we worked very hard on putting together.
Edit- this can hit any item, not just blueprint crafted. It can even hit equipped gear on corpses or npc crew