From what I understand, a programmer typically rewrites the engine maps in the ECU. Some, like the Smarty, store the stock ECU tables in case something glitches in the dowload process.
Why is your truck needing a re-flash? The dealer reflashes usually change some sort of logic or parameters to increase safety, reliability, startup, etc.
Some of these flashes have been to help cam/crank synchronization for faster startup, limits turbo boost until certain temperature is reached, raises idle speed, backup alarm for automatics, etc.
In those cases, your programmer will not do that.
In any case, be sure to return the ECU back to stock programming before the truck gets reflashed, or your programmer may not work anymore.
--Eric