It's a question that's been discussed at great length for centuries if not millenia. If a ship loses its mast, replaces this mast, then over the years has many of its parts replaced, is it the same ship? Although in our case, the ship looks to be almost if not totally destroyed and it is suggested that the ship and its pilot are toast. Ejection pods are entirely upto the discretion of the player and no such pod is seen in-game, perhaps then with this flexibility in RP, we can also assume that enough of the named ship has survived to be reserviced.
It kind of reminds me of 'boss spawns' found in large MMOs. In a lot of these cases, these spawns are said to be unique and the enemy crucial to some plot. The people who have just killed this enemy know that they will just respawn in maybe fifteen minutes, but they still have the satisfaction of destroying that enemy. This relates to something like that of Mon'Star, who is hugely popular and is a kind of unique boss that everyone wants a piece of. Perhaps then, with this kind of ship, we can in RP assume that he hasn't really ever been destroyed however unfeasible it sounds.
Characters whose actions in game reflect on that of their stories however, with both organically working together in some kind of parrellel are more difficult. Surely if they die in-game, there should be consequences in the story. I'd truly think that this comes down to the ship not being the same ship, instead the ship is defined by its captain and although it would not be the same 'ship', it would retain its same personality and identity, unless we go as far as to involve sentimental value. Perhaps placing a captain's name in-game and such could solve this a little more neatly.
TL;DR it's entirely upto the individual pilot, obviously and we could argue philosophy until we've been blown up by lolwuts on the matter.
