We're using RoboHelp HTML version 9 and producing merged WebHelp.
There's no way I know of. You can open WebHelp with the search pane opened, but I don't know of a way to automatically start the WebHelp search. Let alone use those search results in a different system.
Perhaps Zoomsearch can help you out. See http://www.grainge.org/pages/authoring/zoomsearch/zoomsearch.htm