Indeed, you need to remove pak1 and pak2 and mp_bin in order to run 2.55+ on your server.
The etded file contains a lot fixes as it is the ET 3.00 server version.

By the way, it is not connected to ET 3.00 that you need to remove the pak1/2, mp_bin files. You could find the instructions to setting up an ET 2.55+ server on the internet.

/JoNny