You want to setup a scan of SharePoint 2007 that can be stopped and will resume where it left of when the scan is started again instead of starting over from the beginning.
Doing a Native Sharepoint scan with the Network Discover can automatically do incremental scanning. However, if you are wanting to use te Sharepoint scanner you need to modify two config files to accomplish this, and optionally schedule the starting of the SharePoint2007Scanner Service.
OPTIONAL: Schedule a batch script to start the scan
Example configs in VontuSharePoint2007Scanner.cfg to run a job for maximum of 5 hours with throttling set to 15 seconds between import of each batch of documents with a batch size of 10 documents per import.