This team hates you
From Starsonata Wiki
This Team Hates You.
If you attack (or have your slaves set to attack enemies) an AI team, do not expect to be able to dock at the base associated with that team. You will have to wait 24 hours from the last instance of attack before the base stops hating you, and allows you to dock. So- all those commods (that you so carefully gathered) required to bring up that skill level will disappear unless you log off that char and wait it out.