I think signal loss is due to environmental factors not software limitation as beyond about 500kph i started losing satellite locks and beyond 700kph i lost all lock, putting the device right at the window gave me a split second lock reading 930kph but lost it again. Also, while climbing to altitude, altitude readings were stuck to about 150+m. During approach, when the engine was throttled down, altitude started working right at below 500kph and 6000m. So I'm still thinking it had to do with the static or similar effect. Keep in mind I had gps lock before boarding the plane and then kept it near the window for updated ephemeris.
My connecting flight didn't fare any better. Forgot to turn it on and get a lock before boarding and being seated a seat between the window plus the a380 seems to have smaller windows too. So no data from that flight. Would have been fun as it was 12hrs Hong Kong to London.
Ps: I'm using a ublox module with ceramic antenna, typical arduino building blocks from china. I think if the eeprom has not been damaged, part of the code that retrieves the stored eeprom data may have been corrupted which explains some of them not working right.
Edit: the way the gadget was designed, when powered down, there is zero power on everything. uC does not go to sleep mode at power off. Maybe power may have been inadvertently applied while passing the xray machine. Not sure if it has any effect..