First rule ... never file before the IRS starts processing (not just accepting test returns) to avoid this very situation. Program updates happen a LOT in the beginning so if you file too early your return may not be accepted or be stuck in pending until they can figure out how to fix the disconnect.
In my professional program there are updates of some kind almost daily but if a critical one happens between the time I start a return and go to file the return I am prompted to put it thru diagnostics again. This may not change the return on the face but it will fix any underlying issues that could cause problems.
