Hi Drew,
Are you talking about merged .chm files, or merged WebHelp?
What do you mean by "...choosing the merged project link..."?
Are you talking about selecting the subproject book from the main
TOC, or opening the subproject directly from the application by
using a topic in the subproject? There is a known problem when you
open a merged .chm help project using a topic in a subproject as
the initial topic - the TOC doesn't synchronise to the selected
topic. If that's what you're seeing, please post back and I'll dig
out the solution that somebody else offered.
Anne