[jackie_w]

The calibre Editor finds your attached kepub to be full of errors. The main problem being the id values, i.e. id="...". To the best of my knowledge id values need to be ASCII and the first char must be ASCII alpha e.g. id="x123" or id="a1.2".

I must confess to knowing nothing about the use of <ruby> and <rt> tags so I don't know whether they complicate matters. However, I did create a tiny error-free sample kepub from your original kepub - the first 5 links/endnotes only. All 5 do appear to pop-up as expected when I drag-dropped the test kepub to my Kobo. I've attached it in case it helps.