It's only a bad idea if shortening the pipe makes it produce less power in the range you're tuning for. Shorter pipes generally run better at higher rpm than longer pipes and vice versa.
'07 CPB Blue; ZGST windscreen with MRA X-screen adjustable spoiler, tube bar adaptor, PC III, ATRE,BMC air filter, modified stock seat with 2nd Look cover,Scorpion Flame Ti slip-ons, Galfer rotors front and rear, braided-stainless lines, C-F 10R front fender, C-F hugger, C-F inner fairing panels, painted foreman's fins with faux C-F inlay, polished rim lips wired for heated gear and accessories, Givi V35 side bags and E41 topcase with SW-Motech qd mounts