How does Krassis resolve his pilot ability when he has a target lock? Would he use the target lock first then get to re-roll a single dice?

No die can be rerolled more than once.

dont target lock unless the ship is behind you. I normally take recon crew, so I get 2 focus. as odds say you are going to roll 2 hits of 4, and then you have a reroll and chances at focus rolls.

How does Krassis resolve his pilot ability when he has a target lock? Would he use the target lock first then get to re-roll a single dice?

Target Lock and the ability are two separate things but they do NOT interact well with each other. You only get to re-roll a die once so if you do it with the TL you can't use the ability and if you use the ability the TL can't move it.