Hello!

You should stop old Jot Server instance first and then remove Jot Server folder.

How to find the all run instances: 

If you've used forever then you should be able to stop it using command below in the root of the Jot Server folder. 

forever stop app.js

also to find the all instances you can use:

ps ax | grep app.js

or 

ps ax | grep node

It allows to find the all run app.js and then run kill command for the instance from the old folder.

command:

kill -9 pid