IANAL, so maybe the following thoughts are way off. But, it's my understanding that patents are transferred to OIN, and OIN then licenses them to anyone that doesn't assert their own patents against Linux. Now, OIN has quite a long list of patents, and surely Microsoft has software that is relevant to some of them.
So, Microsoft now has the choice to stop asserting its Linux-based patents against TomTom (Microsoft can keep litigating about the other patents), and get a free license to all the OIN patents - probably far more patents than the 2 it was harassing TomTom about. So this would seem to be a rational move for Microsoft to make.
Or, Microsoft can refuse to play ball, in which case it is in violation of all OIN-owned patents that are relevant to its software. Microsoft can't have a license to any of them as only OIN can grant such a license (I think?). This would seem to be a tricky position.