Hello GoldenHelikaon,
Thanks for asking your question here in the Apple Support Communities. I understand how important it is to have all your books sync across your devices. I would be happy to offer a few things you can check to get your books synced.
The first thing you want to ensure is that all your data is safe. You can make a backup in iCloud or iTunes. Use this article for help with that: How to back up your iPhone, iPad, and iPod touch.
Then, I would like to recommend that you do this reset next: If your iPhone, iPad, or iPod touch won’t connect to a Wi-Fi network. Use the section titled 'Still can't connect?' and follow the steps to Reset Network Settings. This brings network settings back to the factory defaults. Then, you can try syncing your books again.
If you still have issues, ensure you are using an open wireless network like your home network. If you are connecting to a free wireless network like a school, work, or other business, the airport, a military base, or a hotspot type of a network, this will not work because these types of networks have high security and high traffic. They do not allow the necessary data back and forth causing issues exactly like the one you are currently experiencing. You can try downloading this over the cellular network by going to Settings > Wi-Fi, and turn W-Fi off. Then, try to download over the cellular network only. Also, third party virus protection, firewalls, or proxies that hide your identity from the internet can cause issues like this. These do not have to be set up on the computer or iPad either, they can be set up on the router. Some security apps also do this, but are only called Security or VPN. There are literally hundreds of such apps that block incoming ports which will not allow this feature to work.
The last thing I can recommend is to try syncing your books manually using iTunes. This article from Apple will help you with this: iTunes 12 for Mac: Sync iPod, iPhone, or iPad. Check the section titled "Keep items from being automatically synced". Once you have auto-sync disabled, go ahead and follow the article and select books, and sync them over manually.
Thanks again and have a great rest of your day.