Changed my whole MS Office from Office 365 /2013 to Office 365 with a new 2016 installation. EPUB-Tools has been completely restored now and is on the ribbon again! I do not know what happened to my recent installation (it was Office 365 with 2013). Checked all my workflow with EPUB-Tools - and it runs without problems.
Btw: op system is Windows 10 latest release, Office is 16.0.4229.1029 now.
@TDR: did you uncheck the tic marks in the Option/Trust Center/add-in part? Maybe you should completely reinstall the Office 2016 and deinstall the 2013 version before if this is not too inconvenient.
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