A Custom App connection can be removed in the same way as any other app connection. Simply visit the Custom Apps view, find your Custom App in the list of connected apps and navigate into the connection.
From here, you can choose to Suspend or Remove the app connection from the Custom App Action Menu, located in the top-right of the app header.
The custom app action menu items
Removing a Custom App
To permanently remove a Custom App, including severing any connections that may be linked to it, choose "Remove App" from the action menu.
You will be prompted to confirm you wish to remove the Custom App. If there are any existing connections established to the app, you will be provided some information to warn you.
Confirming to remove the app