Plenty of people have run no flapper and no programmer.
You're fine as far as not damaging the bike. Only you can decide if the bike runs rougher or smoother at specific times through the power curve.
The flapper mod isn't very drastic. It doesn't change much.
Enjoy.
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2008 WR250X
Gearing: 13t - 48t
Power Commander 5 / PC-V
Airbox Door Removed - Flapper glued - AIS removed
FmF Q4
Bridgestone Battlax BT-003rs