Actually, there has been official errata posted on this very question:
Bumping Ships from The Raiders' Outpost
A question has been raised about how the "Bump Rule" works for the Raiders' Outpost if one or more ships in the original run have been removed, either by the Plasma Cannon, the Orbital Teleporter, or by losing control of the Relic Ship. Does the new run have to be bigger than the original run or just bigger than the ship that are left over?
Here is the text from the rulebook...
You must dock a set of three sequentially numbered ships to use the Raiders’ Outpost. There are docking ports for one set of three ships. If the Raiders’ Outpost is occupied, you may dock a higher-value sequence here and move the original ships to the Maintenance Bay.
While docked at the Raiders’ Outpost you may steal a total of four resources from any mix of players or one alien tech card of your choice from one player. If you steal an alien tech card that you already have, the stolen card is discarded immediately and you gain no benefit from doing so.
Example : If a 1-2-3 is docked at the Raiders’ Outpost and the next player rolls a 2-3-4 then that player may remove the 1-2-3 and dock their 2-3-4 at the facility to conduct their own raid. If another player rolls a 3-4-5 or a 4-5-6 then they may remove the 2-3-4 and dock their own sequence and conduct their own raid.
The addition of a second example should clear up this question.
Example 2: RED has docked a 3-4-5 at the Raiders' Outpost. On his turn GREEN uses the Plasma Cannon to send the 5 back to the Maintenance Bay, leaving a 3 and 4 on the Raiders' Outpost. To dock a higher-value sequence at the Raiders' Outpost GREEN must use a run of three ships that totals more than the sum of the ships currently docked there. The remaining ships total 7 so GREEN may not dock a 1-2-3 since they only total 6. GREEN may dock a 2-3-4 (total 9), a 3-4-5 (total 12) or a 4-5-6 (total 15) to use the Raiders' Outpost.
Errata can be found on BoardGameGeek.