I figured it out based on the above answers, however there is a missing component to the answer, so in case anyone else runs into this issue:
First, open the file /etc/prosody/conf.avail/[hostname].cfg.lua for editing with vim or nano etc.
Find the line VirtualHost “[hostname]” and set the authentication directive to = "internal_plain". This can be set back to "anonymous" once the user is unregistered per step 3.
Run the command: prosodyctl unregister [user] [hostname].
Run the command: systemctl restart {prosody,jicofo,jitsi-videobridge2,nginx}.
That should do it. It’s not clear in the documentation that the .cfg.lua file needs to have the authentication bit changed back before unregistering the user.