Thanks. I followed instruction here
https://www.mobileread.com/forums/sho...=249033&page=3 and elsewhere
I enabled debug-pipeline. In input, calibre changed my aside tag to a div. In processed, it changed epub:type property to epubU0003Atype (sic). The footnote shows up in the footnote pane in the calibre viewer, although the footnote text is visible in the main text. When loaded into kindle PW2 (azw3), I'm not getting popup footnotes, just regular links. epub is a mixed bag: works on google books, not mantano. In all cases, the footnote text is visible in the main book, probably because the aside got changed to div and epub:type is I'm not sure what now.
Any way to make calibre not touch my html? I am using preprocess_raw_html and do not have any remove_*