After I failed the mission, the game still beeps at me when I enter a sector, as though it were a sector where the "mother ship" has been searched for. This is very annoying, and I can't shake it. Changing ships, taking on different missions, I still have the beep. I have no interest in getting blown up by a Trident over and over, and serching endlessly through empty sectors. I retook the mission, failed again, still the beep. I aborted the mission, still the beep. HELP!

Ehum, is it like a dooboop beep? If so that is your proximity alarm, and is just alerting you to the presence of another ship within a certain distance. You can turn this off (and change the distance at which it occurs to a max of 5000m) by opening the sector list while in space (default, u key)

Yarrr! Next dooboop might just be me blasting you, not a Trident ;)