You have not given us much detail to work with and that makes it difficult to give really good answers. Based on your description of a router with ISP A and the collector with ISP B and that it works through the tunnel, then my first guess is that there was a problem with address translation for the NetFlow traffic from the router to the collector. Can you provide the details of how the router was configured, especially the interfaces and the translation?
HTH
Rick
HTH
Rick