Is this an issue that you can reproduce with any regularity? There is not anything in the code that I'm aware of that would update or delete all of these records. Do you have any backups of the db at any point with any of these options?
If you could cause the issue to happen again it would help a great deal in trying to resolve the problem. When the issue occurred were any new products being inserted or was it only options that were being added? The code on the page to manage options has the ability to update or remove options but this code should not run unless it is triggered. Were you present when any of these options were removed from the db? Also, were these simple, conditional, or advanced options?