The easiest way to get through this is to get the correct data from the source, so fix the SQL statement in that it is only giving you the delta records. Now, I am not sure what the source system is, but many ERPs have or should have a "last modified date" field where you can use that in the WHERE clause.
As for Informatica Cloud, I am not an expert, but I would think this would be hard to accomplish as Informatica would have to know (store) the data that was last uploaded and then do a compare and I am not sure Informatica has a storage area. Again, I am not an Informatica expert, so this very well may be accomplished via Informatica.
If Informatica can't do accomplish this, follow the methods in the video.