In another thread davidfor confirmed there is a bug in 4.5.9587 which was causing my problem with the upgrade (post 241):
https://www.mobileread.com/forums/sh...=1#post3569693
If you have kepubs on an external sd card they are re-processed when a card is inserted or disconnected from the pc. Therefore, the downgrade to 4.4.934 is the only solution until they fix the bug.
Problem solved.