The Devs talked about this a while back, and due to the fact that you have to checkout the pilot to your ship, they put it on the object that is your ship, and for some strange reasons, when your ship is destroyed, they looses your pilot!!! so when you are at your rebuy screen, they are have now thrown the object where your pilot is recorded on out the window and so they cannot reinstate your pilot
I find the devs talk about this explanation a bit full of crap, since they still manages to let you buy back your ship, with all your engineered parts, so they did not delete that information. So how come they cannot find the information about your pilot aswell? So the more likely cause of this, they messed up the implementation of your hired crew, and simply forgot to add this function to the rebuy screen, and they know it, and it might get fixed in a future update, until then we have to live with either of these lies:
* Your pilot is top dumb/stupid/etc to get to the escape pod, and is destroyed when your ship explodes
* Your pilot refuses to work with you ever again, so once rescued from escape pod, will always stay clear of you....
Pick anyone that eases your logic of the bad game design and go with it.
I lost a pilot due to I had forgotten that I had my pilot with me and simply pushed the limits a bit to far in a fight, and there goes one Elite pilot... bye, bye... I missed her alot more than then 26 million rebuy of my Anaconda..