How does the number of shuttles in stargate universe make sense?

Ok so In stargate universe (SGU) They start with 2 shuttles. Then they give one to planet "eden". Then one comes back so they have two again then one crashes in episode "aftermath" so they would have one. BUT, in the lava planet episode and the finale they have two shuttles again. Also what happened to all the people they picked up on the planet are they also in stasis chambers?