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Sure removing the baffles could cause you warranty problems. By doing so, you're allowing your motor to breath more. If it 'breathes' more than it can adjust for(adding fuel) then you'll be running lean. Running lean can cause problems instantaneously if it's severely lean(not likely by simply messing with the muff's), or over time if it's moderate.
If you had simply installed sip-ons, generally speaking you usually don't need to re-map your bike. With what you did, I don't know how much you sent your AFR into orbit, so if you want to play it safe, you probably should at least have it checked. FWIW, these bikes run very lean down low, and very fat up top, stock. Lean down low to meet fed emissions standards, and fat up top to save them money on warranty repairs-it's an overreaction, but all manufacturers do it.
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