Well any change to the software updater database would happen through the VPS updates (as far as I’m aware) when there are changes. But yes it wouldn’t be likely that every VPS update also has an update to the software updater database.

That said I think your problem was more than just that, possibly a corrupt software updater database, so there would be no reference, even for installed software monitored by the software updater. So a VPS update with updates to the software updater database may well replace the complete database and resolve the problem.