Or you can assume that everything that has happened up until the point where we journey back in time is the only, true timeline, and our interference in the "alternate" past, creates a branch from that point where new events occur. There are two Velens because we have traveled back to a point in time where we are meeting Velen as he was at that point in time. There is only one Archimonde and one Kil'jaeden because we are not traveling to a point in time on Draenor when they existed there. Their time-shifted counterparts are still active in the Twisting Nether, just as they were at that point in time the first time these events occurred.
Think about it like watching a whole movie, then rewinding about half way and re-recording over the other half of the movie. The entire first half of the movie plays as usual, up to the point you've re-recorded, then whatever you added on plays instead.