Barry Morse decided to leave the series after Season 1 had ended. An explanation of his absence was written into the first episode of Season 2, "The Metamorph", but never made it to the finished episode. Dialog was to indicate he had been in a faulty spacesuit.
The lack of resources is frequently referred to throughout the series. This is contradicted by the fact that throughout dozens of Eagles are destroyed. As they never run out they must be replacing them, the alternative is they have dozens of spare craft on a moon-base.
John Koenig: We've had a lot of success so far. We know what dangers to expect out there from black suns, neutron storms, radiation and the like, but if we think we know everything that goes on out there, we're making a terrible mistake!