InDesign is an old DTP package for fixed layout paper/PDF, fudged for ebooks.
Use MS Word or LO Writer (edit in odt, but extra Save As in docx)
Import docx to Calibre.
Calibre shouldn't have to fudge for one of the worst programs in the world for creating reflowable ebooks. Indesign is also expensive and now can only be rented. Aldus designed it but never released/finished it before Adobe bought them.
What you want is trivial in MS Word or LO Writer using bookmarks (which become HTML anchors in Calibre) and internal hyperlinks.
Use Styles and no direct formatting except words in a paragraph that are bold, italic, superscript or subscript.
DTP is now only for magazines, newspapers and some paper text books (though not absolutely needed for text books now).
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