It sounds vaguely familiar...I don't think the mission shows up all that often, but if I remember correctly, I couldn't find any way to regenerate of enter the drydock either.
As long as this is a generic mission, you can probably leave by esc-forfeiting or flying off the map, without winning any prestige or losing anything. Sorry that doesn't answer your question, I would also like to know how the designers intended the mission to be played out.