'server.cfg' is wiping 'user.cfg'

I'm trying to add a 'server.cfg' file to my cfg folder containing the following commands in order to have a server description and header without manually adding it:

server.description "description goes here"
server.headerimage "image url here"
server.writecfg
server.readcfg

After I put the file into the folder, my user.cfg file containing the ids for myself and other mods is wiped meaning that I only have permissions for certain plugins in the server and it makes things difficult

Any ideas?