I disconnected both batteries in my SL500 and brought them to Auto Zone, they charged them for free then did a battery test. I purchased the battery in trunk ( convenience battery), for 160$, came home hooked it all back up, fully expecting to have to sync the radio, seats and windows. but everything worked fine. But if you have to reset your windows, just roll down and then shut door roll them up and hold button up for about 3 sec and they should reset. if not just try it again holding button up for 5 sec. I have had to do this on my Camaro after I replaced the battery.
I have experienced this same error message and interior system failures upon starting the SL in the morning. After driving to warmup, the message goes away and the convenience features are restored. This is caused by the trunk (convenience) battery being discharged, probably from not much driving in the winter or overuse raising and lowering the top without the car running.
Before you spend the $$$ to buy and replace this battery, check the installation date. Replace if very old, but try to charge the trunk battery (no need to disconnect it) overnight to see if it holds a charge. You can also take the car to any battery retailer, and they will load test it for you, probably free. In my case, the overnight charge did the trick, and all convenience features, including the ability to raise and lower the roof without the car running, were restored. The other blogs on this subject recommend to keep a battery trickle charger (be sure it's the kind that won't overcharge the battery)on the trunk battery during times the car is not driven extensively.
Hope my experience helps you with this. Drive on in the most over-engineered vehicle on the road. But WOW, what fun!