If I am flying a waypoint mission using a 3rd party app such as Litchi, and the aircraft is lost, will DJI read the data log from that app to determine if there was a mechanical or electrical malfunction?  In other words, can DJI only warrant a lost aircraft if it was flown with their app?

That is correct. If you use any their party apps and crash your warranty is void.

Hi there, if the drone is lost when it flies with 3rd party Apps, warranty service is void. And DJI doesn't analyze the data log from 3rd party APP.