Ebooks in Ibooks not brought from Apple won't sync

The books are in Ibooks, they are also in iTunes, when I try and sync they are not added to Ibooks on the iPad

The process I used to follow was I would buy epub books from Baen, I would then add them to ibooks, I would then select all books under the iPad on iTunes and sync.This worked fine up until March but at that point I had my fusion Drive replaced and had to re-install from a backup.

The only relevant support document I was able to find says, "Note: Any books or PDFs you import won’t appear automatically on all your devices. Only books purchased in the iBooks Store appear"

One one attempt, Ibooks on the iPad prompted me do you wish to sync with myemail@me.com instead of myemail@mac.com. I answered yes as my iTunes account on my mac is using myemail@me.com but this did not appear to make a difference.

If its now a manual process what additional steps do i need to complete beyond the process I was doing before?