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Symptom:

An authoritative zone vanishes from a DNS Server configured as being a slave for this zone 

Problem:

There is a bug in some versions of Microsoft DNS Server for Windows Server 2008SP1 (the original Windows Server 2008 release) that can lead to an almost empty zone (only the SOA Record and/or some NS records are shown, but all zone content is gone).

This is an known issue with Microsoft (detected in Summer 2008).
 

Solution

See "A primary DNS zone file may not transfer to the secondary DNS servers in Windows Server 2008" for an hotfix for this issue.

Unfortunately it seems that this hotfix is not distributed via regular Windows Update, but must be downloaded and installed manually.