How can I return a sum of money to a school shop owner whom I was unable to pay back, and who is now missing, and I do not know his whereabouts or his relatives?

If you are unable to reach the owner of the money, give it in charity on his behalf. If he appears afterward, he has the choice between upholding the charity or demanding his money back, as mentioned by Ibn Taymiyyah regarding someone who is unable to identify the owners of unknown funds.