Once you leave the battle tower, some time later the runner will come back on his own. I don't know how long that takes; I had enough gold to fully upgrade the runners right away, so all I had to do was wait for them to leave the battle tower, and then leave and return for them to be back.
Try talking to your trainer and enchanter about upgrades; if the absent runner doesn't show up, I guess you will need to wait until he returns to get him upgraded.
Welcome to the forum.
