open epub book in calibre in custum library
change format to e.g. mobi
copy the mobi-file to another DIR
(deleting the epub-file in library DIR doesn't help, calibre keeps the epub in its memory)
delete the original epub-file from calibre 
(and also from DIR, for security copy it before deleting to another DIR)
insert the mobi-file from its DIR in calbre
that's it