Not exactly sure if this is a NTM or Orion / NPM issue, but I thought I'd give it a shot.
Whenever we export a NTM map to Network Atlas, it wants to re-run the discovery. This discovery automatically adds all of the interfaces on the devices in the map to monitoring by NPM causing us to run over our license limit.
I wish there was a check box that said "don't re-import or re-discover known nodes" when doing the NTM -> Network Atlas map export.