Thanks for the feedback @Krishna Bejawada? and @Duri Bradshaw? .
To communicate with an existing instance of SSA the Applinking/nodejs tool (provided by P/B) needs to be running. This runs in the background and monitors a "Link In" location on your hard drive. If it detects a new link file (in xml format), it responds by reading in the property numbers or other link values and selecting corresponding objects within the specified map layer.
If SSA is not already running, or if you want to start a new instance, the link can be performed via URL parameters instead.
Currently, because a new layer is created each time a link to an existing instance is performed, our client has requested that this feature is turned off. Instead we start up a new SSA instance each time via URL parameters.
We still make use of the Applinking tool when linking from SSA. This works well.
It would be great if the functionality when linking to SSA could be customised to not create a new layer or, as Duri suggests, re-use the same layer.