One of the major differences between ecFlowUI version 4 and 5 is that they can only interact with servers of the same major version. As a side effect if you start up ecFlowUI version 5 you will not be able to interact with any of your version 4 servers and vice versa.
To help the clear separation of ecFlow4 and ecflow5 related settings, from version 5.2.3 ecFlowUI will use a new configuration directory. As a consequence, you can create a separate server list for ecFlowUI 4 and 5.
You do not need to do anything, when you first start up ecFlowUI with a version >= 5.2.3 the new configuration directory will be automatically created for you by copying the contents of the old configuration directory.