The Early Access version of Battleborn uses the same User profile files as the full retail Battleborn. If you’ve played in Early Access, and launch the main Battleborn game, you will NOT see the link to play the Prologue mission, but cannot queue into other parts of the game, because you “Haven’t played the Prologue yet”.
To remedy this:
You need to delete your Battleborn User Profile Folder.
1) Go to C:\Users\<my name>\Documents\My Games
2) Delete the entire “Battleborn” folder in the My Games folder.
If you continue to experience this issue after deleting the profile folder, please submit a support ticket at support.gearboxsoftware.com.