For those who don't understand the timeflows or are questioning it... here is why it makes sense:
Hiro has taken the DBZ way and created alternate futures. The reason destroying the gates worked was because the gate was the anchor keeping past/future in the present. Think of it like a three stranded braid where the one event could lead to any of the three futures, only in this case one of those futures required people from the other two to come back in time and have a part to play to achieve the golden third future that allows them to have a fighting chance. This also explains why that perv dragon (starts with a Z, can't spell it) called himself the Jade dragon before actually coming to the present, up until that point all three futures were possible and had not diverged and thus formed a loop, but the three futures are separate and will always be. This is evident by the fact that future Lucy is dead when she is transported back and is in the golden plains, greeted by Natsu/Happy and her friends, which also means future Rogue went back to his hell.