Missing matrix fields
Nothing in Craft will automatically delete Matrix fields, and there haven’t been any DB migrations that would have deleted an entire Matrix field. (There was a recent migration that deleted some orphaned Matrix block rows in the DB, but that would only have affected the data, not the fields themselves, and wouldn’t have made any noticeable change in the Control Panel.) Someone must have gone in and deleted the field, or changed its name/field type.

If it happened recently enough, there might still be some evidence of it in your logs. We can take a look - just send in a ticket from your Dashboard and they will be included automatically.