I have the same problem like this person (posted on Steam) :

"I don't know whether it's just me, but I had this legendary weapon (mighty hunting rifle) which i upgraded extensively. Thing is, everytime i fast travel with the weapon on. It dissapears from my inventory entirely. Only way to retrieve it back is by loading up an old save. Im sure i haven't dropped it or sold it. Happened twice, just wanted to know if anyone else had this bug."

A normal pistol and a energy pistol disappear from my inventory too - i have no idea why.

I hope this bug is known by Bethesda, so they can fix it.

EDIT: Note: No this isn't the glitch where you can't see your weapon.

It really dissapears from the inventory you cant switch to it because it doesnt exist anymore.

If your weapon disappears, you’ll want to switch to another weapon and then switch back. The weapon that vanished should reappear.

If it doesn’t, you’ll want to revert back to an older save. If that doesn’t work, restart your game or system.