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Our online help is HTML5 generated with RH 11.
If we're viewing the Index tab, and switch to the TOC tab, the index will appear within the Table of Contents, underneath the Contents itself. Why? Did I break something? When we first view the Online Help (with the TOC as the default tab), the index doesn't appear merged there - it's only when we switch to the Index tab and the back to the TOC tab that the index appears merged with the TOC!
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Which browser are you using? Does the same thing happen with other browsers? Does this happen on your local drive and when hosted on a web server?
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Which screen layout are you using and have you customised it?
What you could try is add the layout again using a new name (For example, Theme1_Standard_test), don't copy your existing one, and try generating with that, to see if you get the same behaviour.
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Using a customised version of Theme3_Black. I made a copy (which I stored in another directory outside of RH), deleted the 'suspect' theme, and let RH recreate it from scratch. Regardless the issue remains. ...and I've just discovered that the same issue occurs when switching from the Glossary tab to the TOC - the glossary ends up under the TOC. Odd.
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I had a go with the Employee Care sample project. I added the Theme3_Black screen layout and selected it in the Responsive HTML5 (Primary Layout) SSL. Generated without changing anything else. Copied to a web server and opened in Chrome 77. Everything seems to work okay.
I assume this used to work for you and now no longer does. Try generating one of the sample projects. If it works okay that would suggest it's something to do with your project. If it doesn't work, that would suggest something to do with your computer or the web server.
One thing I'm not sure on. You said you "let RH recreate it from scratch". To confirm, you went in to the Project Set-up pod, clicked the New Responsive Layout icon and selected Theme3_Black from the list?