Here's the breakdown of how this issue has progressed for me over the past many weeks:
I'm an avid reader, mostly fanfiction (i.e. fewer purchased epubs), so my library is a labor of love. I've used Calibre for years to amass my library. After updating to Catalina on my old MacBook pro, any new epubs imported to Apple books from Calibre would not open...error stated it was corrupt (same as an earlier post on this thread). Concerned about my library, I used Pages to reformat my most important books into epubs, (weeks!) added the covers, then imported them into Apple Books. Worked like a charm. Then, because of keyboard issues, I purchased a new MacBook Pro, updated to Catalina, migrated all data from the old mac, and thought all was well.
My spouse had the issue first since she purchases most of her books...new epubs would import to Apple Books (on her MacBook) and open just fine. However, when syncing through Finder, while the new books appeared on the list and were selected, they will NOT sync over to any device. No error message at all, just no new books. UNLESS...you make it a PDF. However, while PDFs sync over, they do NOT sync across devices for annotations or place keeping.
Last night, I had to edit an existing book (previously synced to ipad pro and iphone 8 plus). I deleted the old versions from all devices and Apple Books (Mac), then imported the updated epub to Apple Books. It opened just fine, but would not sync to my iPad or iPhone. I ended up having to use the PDF version.
Seriously, this could very well be the final straw for me. Over the past several years, it seems Apple has become lax in its care and maintenance of the Books app. While it may not be the most popular app, that's no reason to let it fall by the wayside. Considering many of us have invested YEARS of work and loyalty, not to mention the money, it would seem logical to be more proactive and diligent.
I've had repeated issues that almost never get addressed, leaving me to find workarounds. Apple, we shouldn't have to work so hard to use what we've relied on for years. Please, fix this.