Thanks for the info.
About the kepub conversion due to KoboTouchExtended, I will test this evening.
About the "random" popup, if what you say is true (# anchors links will trigger a popup) (well, at least when going forward ... and some other times), to avoid this behavior for non-footnote links I have to split each link destination into a new file. This can be done (all links are new sections), while a little tedious... By the way, I will test with a simplified version of my book.
About this, is there a way to sort the files in Calibre Editor by name automatically and not manually by drag/drop?
Last, about the sample epub I've attached, have you tested without kepub functionality? The problem is that even for plain epub, forward links will show the toolbars (not the popup like for kepub).
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