I have a brand new battery in my 06 s430. Ive been converting the suspension from airmatic to stutmasters coilovers. Its been 3 weeks since I was able to have time to get back to where I stored it and finish it and the battery was completely dead which is understandable being so long since I started it. Well I jumped it off after finishing the conversion. Drove around about a hr took it to car wash and all that. Well all of a sudden the red battery charge warning came up the command center turned itself off and the car went into limp mode. I was able to limp it to the shop I work at now parked it. By this time the dash was black I couldn't even turn on the hazards. I shut it off tried to turn it back on and off course nothing. I used to start it every weekend and let it run for 30 min never had a charge problem. Could it be now that I had it back on the street the alternator is now messed up maybe from jump starting it. Not sure it was weird it did fine the whole hour I was driving even turned it off at a store went in came back out restarted it no problem. The charge issue just happened while driving? Any suggestions would be appreciated

Unlike other simple cars where you can just jump the car and let the alternator charge the battery , you can’t rely on the alternator to charge a fully dead w220 . You may have over stressed the alternator .

you need to use a dedicated battery charger to charge the battery to full charge , then test drive it

As tusabes says, fully charge the battery. Before doing so, check the battery terminals for corrosion or looseness.

Check the battery voltage - should be at least 12.6 volts.
Start the engine, and check the battery voltage - should be at least 13.6 volts. If not, there is a problem with the alternator.