The problem is that you were still on an affected version 3216. By upgrading to the newest version the Stablebit Scanner Service is forcefully shut down, thus the DiskId files can get corrupted in the upgrade process. Now that you are on version 3246 which fixed the problem it shouldn't happen anymore on your next upgrade/reboot/crash.
I agree wholeheartedly though that we should get a way to backup the scan status of drives just in case. A scheduled automatic backup would be great. The files are extremely small and don't take a lot of space so don't see a reason not to implement it feature wise.