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.
Add the MaximumJobTime to the Job0 section. The value is the number of seconds to run.
Set the ImportPoliteness if desired. This is the number of milliseconds between requests.
Set the BatchSize if desired. This is how many objects per request.
Set scanner.incremental = true
OPTIONAL: Schedule a batch script to start the scan
Create a batch file with these contents: net stop "Vontu SharePoint2007Scanner Service" & net start "Vontu SharePoint2007Scanner Service" (this will stop the scan if it's still running and then restart it - resuming where it was last)
Schedule a task using the Windows Scheduled Task utility to run the batch file every day (or week/month/etc.) at the desired start time
Schedule the Discover target on Enforce to start at the same time. This allows the incidents detected by the SharePoint scanner to be relayed up to Enforce instead of building up on the Discover server.
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.