I don't know what to tell you -- they're there, and I can open and view them. I'm highly doubtful that anything malicious is on my computer, much less deleting autosaves.
Yep, the pauses are pretty painful. The crashes usually happen towards the end of the flight, and often occur when I try to use manipulators, but the cause remains unknown to me; it's just reported as ntdll.dll. As much as I don't want to, I may end up reinstalling P3D, despite the serious cost of time. I do need to solve this issue of the crashing in the first place, but I thought it would be helpful to bring my experience with the issue to light. Unfortunately, I can't really test to see if it's limited to PMDG aircraft, as I don't really have anything else that's long haul.
Anyway, I will reinstall P3D and install the update as well. Thanks for your help!