The ISS orbits the Earth every 90 minutes and NO-44 is in a polar orbit, so unless your balloon is really
moving, it should be in a position to be heard by one or the other several times during the trip over the Atlantic.
At that height I would think your chances of being picked up by a satellite would be much higher than a ground station. It would be an interesting experiment to see if using satellite APRS exclusively would work, but I'm sure you'd rather see reliability over experimentation when it comes to telemetry.
How complex is your controller? I could see testing the balloon location against a boundary that could then switch in a different crystal in a radio something like this: http://tinyurl.com/bbzq4k3
(Google conversion of a Ramsey 2meter crystal controlled FM transmitter manual). There's not much available that would be simple enough to be switched unless your controller is fairly advanced. In fact the only small agile synthesized transceiver that can be remotely tuned "off the shelf" I can think of right now is the FT-817.
Maybe reach out to Byonics.com and see if they have any way of changing freq on their beacon radios. Don't forget that your TNC will also need to have a different path (ARISS) for the ISS and NO-44 to digipeat.