If you are hoping to keep all the users, while only deleting 1 user, there is no need to go through the harsh time consuming process of "./eggdrop -m <config.>file"
You can just type ".-user <handle>" in the partyline. You will need to be an owner yourself on the bot to do this.
If the owner is set as a perm owner in the config file, this makes things slightly more tricky. Edit the config file, and remove them from the owner setting. Goto the partyline and type ".rehash". Now you can o the .-user command.