I had a similar experience with my '98 E300 diesel. I bought a new battery and put it in my trunk. I went home and took the old one out and tried to get access to the new one. The trunk would not open until I reinstalled the old one. There is something electrical; I don't know what it is.

There may be an alternative I didn't try. My key has a small metal key that is inserted into it for storage. I have been told that had I had the sense to use that metal key, I could have opened the trunk without reinstalling the battery. Try that first if you have one.