I think you should change SkyVia Replication to track the LastSyncTime on a per object within a package basis.
I also thin you should change SkyVia Replication to perform all replication to a target database table within a database transaction. This way, you would not partially update a target database table in the event of an error.
By combining these two changes, you should be able to guarantee data integrity of a target database table as of a successful last sync date, These changes are necessary to move SkyVia Replication towards being enterprise-class.
I look forward to your reply