Just do it !
But I've only repaired four of the six damaged areas on the ship. How can I go on to Scenario 3?
If I'm supposed to repeat Scenario 2 until I succeed in repairing all six damaged areas, how can I do that since everything has changed on the board?
You mean the other two ship parts are not repaired at all?
Look at the table for "Critical Level Effect" for scenario 3.
Two ship parts at critical level at the beginning of the scenario will make you lose very early.
Every ship part should be reapaired at least at minimum level.
So better start scenario 2 again.
That means you should keep track of the scenario 1 end conditions.
If you didn't do that, hmmmm .... then you must start all over again.
But you gained experience and will play more efficiently