Alright Sheikarah let me explain everything.

Your chip made it unable for Ellie to track your ship, but she scanned previous readings of Hessta's ships and knew the basic layout and appearance. She then scanned cameras to see if she could notice a similar ship, and she did. She realized it was heading for Corvais, so she started scanning Corvais cameras and she found the ship there. She is unable to lock on to it since the chip make sit 'invisible' on her radars, and as such Six must manually follow you.

As for everyone else... glad to get moving again.