Fallout – Fast Travel glitch in fallout 4

There are still a few options; Keep your best equipment and power armor in a depopulated settlement, such as Red Rocket truck stop. If you haven't sent settlers there, then settlers can't steal your equipment. Raiders may still be able to steal your things, but that's what all the turrets are for, right? ;)

Alternately, find a safe connected to a terminal, drop your stuff in it, and lock it. This has the downside that you'll have to travel back to wherever the terminal-safe was. And even if you can find or somehow create one in a settlement, settlers that have the hacking or lock-picking skill might still be able to get at your things.

Optionally, keep all your things in a region of the map inaccessible to settlers, such as a rooftop or closed-off upper floor with a welcome mat. This ensures that you can fast-travel to the area, while your settlers won't be able to reach it.

The closest I found to a workaround for this issue was to reload an old save, from before I had manually attacked the Prydwen. After doing that, I found the Underground Undercover quest progressed correctly with the following in-game state:

1. Glory is alive.
2. BoS members on the airship are alive.
3. BoS members on the ground at the airport are alive.
4. Paladin Danse is dead.
5. The 'Underground Undercover' quest wants me to warn Desdemona.
6. I haven't progressed the 'End of the Line' quest past the point where it wants me to talk to Father.

After that my game worked as it should (got to fight off the BoS attack, got the mission to attack the Prydwen, looted Final Judgement off of Maxson's corpse, was able to warn Desdemona again after talking to Father, etc.).

Another interesting thing I found was that if you progress Underground Undercover to the point where it wants you to clear the control room, you can instead turn around and take the elevator back into the Institute proper and pick a fight with everyone without getting banished. Among other things, that lets you take out members of the directorate and other named Institute NPC's who disappear if you just keep progressing Underground Undercover.