What exactly do you mean by “change the name of an instance”?
For connection purposes the Rest API (Apliqo UX included) doesn’t care about the name of the instance at all, the connection URL (the IP and assigned http port) is the only thing that matters. As the IP or port could theoretically change between sessions internally in the content store UX uses the name assigned to the connection URL as the key to reference the datasource which the widgets will connect to to retrieve data. This means that migration is a non-issue as all you need to do is define the same instance name in the instances.json between environments.
I’m not sure why you would wish to change the name in the instances.json for a reporting instance as this is really an internal reference for UX. It is never exposed to end users except when selecting a data source for a widget in edit mode. If you had an existing application and you renamed an instance in the instances.json file then you would need to run the find/replace utility in the content sotre to update names before the application would work.
Note you cannot ever rename the content store. It must always be named “contentStore”. Otherwise nothing will work.
To rename the whole app (the URL where you connect to UX) you simply stop the apliqo application server and rename the folder in the webapps directory and restart the service. Simple as that.
So back to the question. What exactly are you trying to rename??