If your stick is connected to a USB hub the USB ID may be changing if other devices are connected to the hub. Then the game no longer sees the device you mapped previously. I've had trouble with that and avoid connecting HOTAS to hubs.
Sorry I'm late to this party but just had the same happen to me. It happened right after I moved my VKB gear to a powered hub thinking it would be convenient. It wasn't very convenient as I sat on the runway like a dope frozen in amber wondering what was going on.
Anyhow, came here and found this thread and followed both AKIron and Drano's advice. We'll see how it goes.
I don't have virtual yet so my config files for saving were in settings and were named VKBSIMGLADIATORxxx.JSM.
I had windows setup not to let USB devices power off but an update reversed those settings it seems so that may be part of the issue as well.
Sorry for the re-dredging of this thread.