Just found this morning the option to select on a book by book basis whether to convert to kepub or not

Great feature.
If like me you haven't seen it, go to
Preferences |
Plugins |
KoboTouch |
Customize plugin. On the
Collections, covers & uploads tab select the option to
Use Kobo viewer for EPUB books and then in the
Template to decide conversion enter either
{tags:str_in_list(\,,as_epub,false,true)} or
{tags:str_in_list(\,,as_kepub,true,false)} depending on whether you want to only tag books to leave in EPUB format, or only those to convert to KEPUB.
Depending on which template you use, either tag ebooks with
as_epub or
as_kepub.