We have successfully modified SCCM software inventory to compare the deployment result to a webfarm.

However, our issue appears to be that the total row of data gathered is increasing every time the scan is done.  Is this because the SCCM is repeating and keeping the same scan data as new entry in the database ?  Or, is it that the scan was not complete last time it ran and it is continuing to pick up from where it left off since last time it scanned ?

What is the logic in keeping the scanned data ? 

Without your query no one can answer this question. It would be a guess at best.