How can the plot of Hiveswap happen? Didn't the Trolls featured in Homestuck create the human's universe when they played Sgrub, meaning the universe doesn't exist at to the Hiveswap trolls? Am I missing something?

The Machine that teleport Joey and Dammek also transports them through time.  While Hiveswap takes place in 1994 on Earth, on Alternia it takes place an undetermined number of sweeps before the start of Hivebent so possibly anywhere from 7 to 20 or more sweeps.