GPS Good to go
From BeeLine GPS User’s Guide:
17 GPS Module Limitations
The GPS Receiver firmware contains an algorithm that allows either the speed limit (515 m/s) or altitude limit (18,000 m) to be exceeded, but not both. This allows the receiver to be used, for example, in high altitude (research balloon) applications.
So as long as the speed stays below 515m/s you should get good high altitude readings.