Why the people of the Elite universe decided not to put these poor chumps out of their misery when they invented the hyperdrive is anyone's guess. I can't imagine the look on their faces when they finally arrive at their destination, only to find it's been settled for a thousand years already...
So, the hyperdrive's just been invented. Someone remembers that they really should go and get the generation ships caught up. They fly up to the first one they find, find there's been a malfunction decades ago - everyone's long dead.
The second one they find is still intact, and they dock - but the crew are culturally centuries behind current society, and the realisation that they've as a society spent two hundred years in bleak sunless space, eating endlessly recycled food and water, living and dying in spaces the size of a box ... not so that their descendants could reach a new world and bring humanity to the stars, but so that someone could say "wait, you lot, we've got a better idea" and the whole journey was pointless ... that really hits them hard psychologically. The shock is essentially fatal to the inhabitants, and that really shakes up those involved in the rescue, many of whom quit their involvement with the project.
The third one gets discovered ... they decide to leave it for a little bit, and try to work out how to make a better job of it than they did of the second one. The usual bureaucratic indecision occurs, humanity as a whole gets distracted by the new settlements springing up on Sirius, on Barnard's Star, on Ross 154 - with the huge increase in prosperity as the price of formerly rare minerals falls.
By the time anyone gets round to coming up with a plan and someone to fund it, they realise that on top of everything else, they then will have to explain to the ship inhabitants not only what's happened, but why they waited thirty years to tell them, and the whole thing gets quietly shelved, the pre-Federation government pragmatically assuming that:
a) almost all the ships will suffer some sort of fatal malfunction before they reach their destination
b) in the event that one doesn't, it really really really won't be their problem.
'b' is, unsurprisingly, also convincing logic to modern-day governments, and the generation ships are assumed to have nothing worth salvaging for the even less scrupulous types.