The ECU will adjust the closed-loop A/F ratio automatically, within limits, and the open loop map should be close enough unless you made a radical change. But be aware that fueling is only one thing that is affected by an aftermarket exhaust. Cam timing, ignition advance curve, etc. are set up expecting an OEM system so any major changes to intake or exhaust can easily lose more power than they gain, and without a re-tune that is frequently what happens, or power is shoved around a bit withing the powerband so you may have a net increase at one engine speed and a loss a net loss at another. Which was best, before or after? Anyone's guess unless engine performance is addressed as a system since there is no guarantee that changing a single component to a 'performance' version will do very much unless the OEM design was significantly lacking, and this usually isn't the case with BMW bikes. The slant-K bikes in particular are tuned pretty highly just as they come from the factory.
Anyway, to your situation, since the OEM maps are on the lean side to meet emissions regulations then reducing backpressure can serve to make that condition worse. You may have a lean stumble, not a rich condition. If that is the case one of the preset fuel enrichening devices might help (kind of a shotgun cure), or better option would be to install a Power Commander and have the open-loop map properly tuned on a dyno. All-in-all a PITA for a maybe few more hp a high rpm, which is all you're going to get even under the best conditions.