Scarred ships: When a scarred ship is deployed, it must choose and discard one defense token.

General Tagge: At the start of the third round and the fifth round, each friendly ship may recover 1 of its discarded defense tokens.

So is there any reason why Tagge wouldn't be able to get a scarred ship's defense token back? It seem like a slam dunk, but I wanted to make sure I wasn't missing something.

It looks ok to me. As you say the rules are clearly written both using the same terms with one reversing the effects of the other.

Obviously if by turn 3 a scarred ship has lost a defence token through overuse, NK7s, Nym or a critical effect then you would have to choose to recover it or the one from the beginning of the game.

Driving your scarred fighters straight onto the space station is also a valid tactic. On that a canny opponent may anticipate and plan his actions accordingly.

I assume that if your scarred ship or squadron survives the battle and is still not repaired in the campaign the scarred effects are reapplied in the next game even if you replaced the defence token or repaired the squadron on the base.