I would guess that MC silently reimported all of your files after thinking that they were all "gone". This normally happens when you have the files on a drive that might not be there all the time. Like a removable drive, or a NAS that might not be turned on, or ready by the time that MC starts.
That, in conjunction with MC's setting to "Fix broken links" would delete all of your files, if the drive wasn't available for some reason. Then, next time the drive was available, MC would auto import them all again, but not in the original order.
I would suggest restoring a recent Library Backup. MC makes them automatically every few days. File > Library > Restore Library
Then I would suggest setting Fix broken links to NO:
Tools > Options > Library & Folders > configure auto import > tasks > Fix broken Links > NO
Good luck,
Brian.