Just speculation, but this seems relatively straightforward to me. Nike reduced his contract, either to a lower dollar amount or just gear. He would be foolish not to wear it for training, given the amount he would go through as a professional distance runner, but he therefore does not want to market it anymore. It hasn't just been the shoes, it has been gear too. Most posts of his either obscure the swoosh or he wears something different all together, like the picture in a RunGum singlet.
This is a classic situation that we have seen before with Nike runners. Nike is running a business, and they need to decide who to pay and who not to in the all-important Olympic year. If you were running the sports marketing group at Nike, would you rather sponsor an older runner with a history of coming up just short of making the team, or a younger up-and-coming runner with unknown potential?
I post this as a huge Will Leer fan, but also one with the realization that this is a business, not a charity.