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Yeah I hate this limitation. My workaround:
I like for each page in the EPUB to have a breadcrumb trail at the top of it, but I don't want that in the original InDesign document. What I'm doing is creating a text box with the information in it and placing it outside the page but touching the page. It has its own paragraph style in it (which does not appear anywhere else in the document) and I'm telling InDesign to break at that paragraph style. That allows me to break at all the chapter beginnings, title pages, etc. because the EPUB picks up anything touching the page. So, for example, in the margin on one of my pages, I have a textbox that reads "Contents > Departments > President's Message." That doesn't appear in my print layout, but when I export to EPUB, it comes in at the very top of a new page.
So that might work for you (?). At least if you don't mind having a little bit of navigation information at the top of each page (I have it in small text above the header). It might be possible to do it with a paragraph style and NO text though I haven't tried that.
Hope that helps.