Even if Amazon wins there will likely be a re-bid process. At which point they will simply select Microsoft again. As we've seen with the DOJ Trump can exert significant influence without having to actually tell them what to do.
See the KC-X tanker program as an example:
01/2007 - RFP comes out
02/2008 - Northrop Grumman wins
03/2008 - Boeing successfully protests
08/2008 - Revised RFP comes out, then cancelled
09/2009 - Third RFP comes out
02/2011 - Boeing wins
Someone at Oracle with access with Trump brought it to his attention, and Trump personally intervened, ordering DoD to ensure Amazon was not favored for the contract.