Question: do the logs show actual stick control used (left up/down) or only the function assigned?
I ask because if only the function applied is shown, then there could be an issue with stick assignment. I mean it is assumed left stick up meant throttle up. Perhaps that wasn't the current assignment. If instead right/left stick assignments were reversed, or left up/down were reversed, one could get confused on what they are commanding. They think they are applying throttle down with left stick down, but really it is applying throttle up or move forward/backward.
RC calibration: that could explain commands sent with no actual stick pressure, but that only biases the command from zero. You can counter that. IOW if stick neutral sends 10% up, pushing down all the way would still give you at least 90% throttle down.
Assuming throttle stick did become useless and not sending proper command. Command to land to get lower altitude and cancel when low enough to get out of high wind. Then use right stick only to bring her back. In case of orientation confusion map should show if you're heading closer back or not using thrust and bank.
Use yaw only if map shows stick use matches command.
Max Height setting could be used to prevent going too high even autonomously, though I don't know if you can have the change take effect mid-flight, particularly if you've already gone above the new limit.
Of course these ideas are easy to say after the fact. Much like answering game show questions in the comfort of your home vs being on the show.
The plus side was that signal was not lost the entire time, so there always was a chance a solution could be found, but sad that a solution could not be thought of in time.