To be clear, there's a lot that goes into what becomes a controllable GPS chip (specs, usage, who is using it, etc.), My prior comments were meant for a high level explanation, but I guess it may merit more detail.

I can't speak to the exact phones or app to which you're referring, but accuracy and timing lag also play a big role. You may be able to get a "lock" but the +/- accuracy may be outside the controllable scope. Alternatively the "real time" data from the chip may be delayed by such as to be outside the controllable scope. In other words, there are other ways to make a GPS chip inaccurate enough that it can't be used for nefarious reasons without literally turning it off.

The OP could have had a chip that just stopped working or fed information so slowly as to appear inoperable. While I will concede its possible to have line of sight issues with GPS signals due to material composition of the plane, I have many experiences in which my phone's GPS works properly on the ground in the middle of the plane but not while in flight.