Guild Wars 2

When playing the “Setting the stage” storry mission with a friend, my faction changed to his (from vigilant to whisper) and i can´t change it back

This is not a bug, but working as intended. When accepting another player’s Story instance progress, in order to allow you to continue to play with a friend, the game will move you to their Story arc.

You can move back at the end of the Story level arc by avoiding accepting another player’s progress.

Good luck.

Yes but I completed the last mission without my friend and now it says my lvl 50 story line is the whispers and I can´t play the vigilants lvl 40 story

You can never go back and repeat any Story episodes.

You can create a different character and choose that arc, should you desire to play that story line.

Good luck.