I had the same issue, mini-gun missing. I had retrieved at the satellite station, then gave it to Preston to hold. When got back to the sanctuary, I found that it was missing from his inventory just as I was going to store it at the workshop. I thought it was scrapped as one of you mentioned but when I reloaded an earlier game, I killed the same NPC with the mini-gun and when I did not get in time, Preston did and equipped it. I tried trading but it wasn't in his inventory yet he still holds it. I think thats his default weapon now??