OK, if you are SURE the battery in the remote is good and you have reset the remote using the instructions in the owner's manual then the blinking lights may indicate something is amiss with the ignition lock-out system. It is described a little in the owner's manual. If you engage then disengage the lock-out, it might get it back to normal. Try this. While sitting in the driver's seat, first, lower the driver’s window, then, lock the car with the remote, unlock the door with your hand(don't use the remote), open and close the door. The ignition should be locked-out. This is an anti-theft feature. Try to start the car. It should not start and both mirror lights should blink. Now, get out of the car, close the door, and lock/unlock the doors a couple of times using the remote. Everything should be back to normal, i.e. only one of the mirror lights goes on when the remote is used and the car will start. I tried this in my '96 C280 with no problems. If there IS a problem with your lock-out system, it may not respond normally and, I suppose, you could get permanently locked-out. Then again, a good time to discover any problem would be at home under controlled conditions and not stuck out in the boonies somewhere with your ignition accidentally "out-to-lunch". Even better would be in the parking lot of your nearest friendly MB dealer...just in case.
Good Luck, Dan