I have followed the documentation very carefully before asking for help and I followed it again after you suggested it. I am doing exactly what is recommended but it is still throwing a bogus error. I know this error does not make sense because when the Where clause is not met, the import works correctly. It is only when the where clause does match up that it fails.
Here is the query that was sent by the import tool kit to kentico to get the matched rows.
FROM View_CMS_Tree_Joined AS V WITH (NOLOCK, NOEXPAND) INNER JOIN Info_Site AS C WITH (NOLOCK) ON [V].[DocumentForeignKeyValue] = [C].[SiteID] AND V.ClassName = N'Info.Site' LEFT OUTER JOIN COM_SKU AS S WITH (NOLOCK) ON [V].[NodeSKUID] = [S].[SKUID]
WHERE (SiteExternalMasterSiteID = '600')
This query is also followed by a number of SELECTs and UPDATEs for the various kentico tables in relation to this import. So it acts like it is moving through the process but still throwing this ambiguous error.