I have noticed that while you click Disconnect button at the main Ekos panel it immediately activates Stop INDI button (which normally stays disabled while you have any device connected). I believe Ekos should wait until all devices are actually disconnected before activating Stop INDI button. This especially applies to devices such as focusers, which need time to travel to park position and if stopped while in motion they are in undefined absolute position.
Implementing this would have to take into account a timeout for disconnecting devices for drivers that freeze in some abnormal cases. Otherwise the Stop INDI button will never get active. What do you think?