I've now reinstated the BIND zonefile directory in the DB. It is strange that the value got deleted. There is no log of any user apart from the ispconfig user accessing the DB and all access correlates with modification of site values. The only person using the system was a reseller who does not have access to system settings.
On a separate note, one of my resellers has (inadvertently) found another way to break BIND through ispconfig. When entering a new site, if you trail the domain by a period '.', it will not create the primary record and will prevent named from loading.