I think you are making a mistake going for HTML5 rather than frameless. Customisation is very limited in HTML5 but extensive in frameless. If you later come back saying you want to customise things in HTML5, the likely answer will be you can't or it's very difficult.
Also going forward Adobe will be focussing development on frameless outputs so I recommend considering frameless templates for your project. Other than bug fixes, it is unlikely there will be any changes to HTML5 outputs. The calls for frameless outputs are different using URLs so you need to discuss that with your developers if you use context sensitive help.
You have to upgrade each project in the merge and then create a new TOC with links the child project in rhpj format. The topic will be the default topic in the child project.
This is all described in the merge topics on my site.
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My site www.grainge.org includes many free Authoring and RoboHelp resources that may be of help.
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