Hello!
Jot Server it is server's app which allows members to communicate  in Messenger in real time. In other words It allows to see that the user is typing a message or away or update your chat window without messenger's page reloading when you get new message.

Jot Server doesn't store anything in local server's files and in addition messages are not sent through the server. So, Jot Server just redirects commands from members in Messenger to update the chat window.

The all messages store in site's database and Jot Server don't see them and doesn't save them.