How I did it:
1. Copy Character [email protected]
2. Load up the character on Tribble.
3. Beam up to Sol (system space), and find abilities for the U.S.S. Helena (Guardian Cruiser) not where I want them.
4. Open up Abilities Window.
5. Uncheck "Lock Tray" in the Abilities Window.
6. Rearrange Ability Tray so abilities are where I want them.
7. Check "Lock Tray" in the Abilities Window.
8. Close the Abilities Window.
9. Switch ships to the Firebird's Dance (Risian corvette).
10. Find abilities where I had and wanted them them prior to DR (except the missing battery in slot 5).
11. Switch ships back to the U.S.S. Helena (Guardian Cruiser).
12. Ability tray has reverted to how I do not want it.
I hope this helps find the problem.