You can register new application instances on the Synergy portal as a system administrator of ChemAxon Synergy. A registered application always has to belong to exactly one team, so application registration can be initiated from the team's page.
In order to access a team's registered applications, you need to open the Teams tab first, then click on the team you wish to modify. At the bottom of the next page, you'll see the list of the registered instances. Click on remove to delete the application instance.