In order to have a working theory of time travel and avoid paradoxes (like killing your own grandfather) you have to assume that time travel causes alternate realities. If we assume just one reality for SGU then we have a paradox, because the discovery of the time-traveling kino prevented the events that lead to said kino being sent back in time in the first place. Since there seemed to be no paradox we must assume that SGU has alternate realities spawned by time travel (and perhaps other things).
So in what we'll call "Reality A" the team went through, got completely shredded by the disease and the creatures on the planet, and Scott sent the kino through the glitched wormhole. This created a second reality, which we'll call "Reality B". In reality B the kino lay forgotten for a long time (long enough for a body to decompose) until this reality's crew of the Destiny came along and found it. The crew managed to handle themselves a little better this time, but ultimately Scott was still the only survivor planetside and sent the kino through the glitched wormhole again. This created a third reality, "Reality C". We did not get to see any of what happens in reality C, but presumably things went much better off for this reality's crew of Destiny, and also presumably this reality is what will continue forward for the rest of the show (unless there's another time travel episode).
If you followed all of that, logically the kinos from reality A and B each traveled back in time to a different reality (kino A went to reality B and kino B went to reality C), so that means that there shouldn't be two kinos for the crew of reality C to find.
Of course, there's a second theory of time travel that says that you simply cannot change the future. Paradoxes don't happen simply because they can't. This doesn't seem to be the case with SGU because they did change the timeline by sending the kino back.