Secondary windows are troublesome in CHM files. You can make them happen, but not without expecting to jump through some serious hoops. I used to use them all the time. Then the hoops were increased and now I just abandon the thought.
Assuming you still wish to use them, I think you do it by using a Related Topics control. RoboHelp will not help you with this. In fact, it will hinder you.
Drawing from some distant memory, I think what you do is configure the control to believe it's opening a second CHM. I believe I've documented the process in my Tips file. You may download it freely from my site at RoboWizard.com.
I downloaded your TNT and what you describe for the Secondary Windows is exactly what I need. My problem is I have no idea which links in my .htm pages are links to other topics and which used to be secondary window links. I'd have to manually open the old.hlp file and compare every single link and fix them manually. My links to the other CHM are easy to identify based on the link but nothing distinguishes the other links. I had hoped RoboHelp was a little more intuitive during conversion. We think it might have something to do with the window types in the .HLP files but we haven't dug deep into that theory yet.
As for the first half of my post... my popups need to point to a different CHM for the contents of the popup (like a Glossary), kind of like Text-only popups. I looked at Peter's site regarding Merged Help (there is a section on CHM) and added the Glossary as a Merged Project. I then inserted a popup to a local topic in my project. That link worked fine but then I swapped the URL in the BSSCPopup call to point to the other CHM topic, compiled, tried it and it can find the Glossary topic but it's not opening it in a popup, it just opens it in the frame.