Some Books from TOC are missing when generate to Microsoft HTML Help

Which update of 2020 are you using? 2020.8 is the latest. See Update 8 is now available - Adobe Support Community - 12693168

Is the correct TOC selected in the preset.

Also is a condition expression applied in the CHM preset?

Beyond that I can't readily think of a reason but I'm happy to take a look at the project. Can you share the project? If you can, then see the Contact page on my site and send the project as instructed there. Do make sure you include a link to this thread and please do not email the project direct.

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My site www.grainge.org includes many free Authoring and RoboHelp resources that may be of help.

Well, there doesn't appear to be a topic attached to that page in the toc (the Source field is blank). If you link it to the correct topic then that page should appear in the output correctly.  

If you haven't made many changes since you upgraded, can you try the upgrade process again? Perhaps another attempt will upgrade the toc correctly. 

If you can't try to upgrade again then I think you'll have to redo your TOC.

Can you expand a couple of the books? Are the topics attached correctly? Are there any symbols on the topic references?

Did you import or upgrade? You should have used the option to Upgrade Project rather than importing topics. If you imported and have only just made the switch and haven't really changed any content, you could try the upgrade process to a new folder and see if that works correctly.

If you imported and have made content changes since the switch, don't worry, we can see if we can figure out the problem.

To the specific missing folders, if you click on one of the missing books in the table of contents, check the properties panel to see if "Hide in output" is selected.  This setting ensures content is included in the output, but does not display in the table of contents. If it's set, then unselect it and repeat for all books and topics. Theoretically you would have had to specifically set it, but stranger things have happened.

Beyond that, I'll have to have more of a think about what else to check.

Do you have condition tags defined and a condition expression selected in the output? That could be excluding topics with particular tags from your output.