As far as I know, they didn't actually apply damage from red scenarios. They only deleted those that were destroyed. I still have the YT2k I flew in the Nar Shadda battle, and it was severly damaged, but that was never reflected in the database.
It is possible that some GMs did apply damage, but I doubt it. Nar Shadda was one of the few actual space battles that took place. If they didn't apply damage to those ships, I doubt they would have on any others.
And From A Darkness I Descend
Clenching A Torch Of Sweet Revenge
A few years back, interdictors were enabled and could block entire systems with gravity wells. To prevent players from being completey trapped in a system in such a scenario, the option to jump into hyper from a gravity well was implemented and included a chance to damage your ship during the initial jump. I damaged a few light freighters that way.
It was discussed at the time and determined that the distance between two adjacent systems would require years of travel time to go between. Hence the jump from grav well and take damge was introduced instead.