Good going using the syringe. I would fill the reservoir with fresh fluid and use a vacuum to draw out the brake fluid. I think a mighty vac tool would work well. Make sure you close the bleeder once your were done drawing the fluid out. Also, keep filling the reservoir as you went along with the flush. Donít let the reservoir run dry. Iíd inspect the fluid for any additional contamination once you were done. After the flush, I would then bleed the brakes using the brake pedal on the bike. Since the use of the front brakes are linked to the rear but the use of the rear brake isnít linked to the front, you may want to flush the front brakes as well. Why leave cross contamination to chance?
If Iím not mistaken, the fluid in the abs pump wonít be flushed out during this flushing process. Now I have very limited servicing experience with bmw motorcycles but I suspect these vehicles use a diagnostic tool to cycle the abs pump to flush out the fluid. So, depending on how bad your contamination is, you may want to have a dealer do this for you. Itís a judgment call.
If I found this situation on my bike, I would flush the heck out of both the rear and front brakes. Then I would perform the final bleed to the entire system by using every bleeder screw using the force of the bikes master cylinder.