I'm sorry to hear that your files were lost in transit from iCloud to Dropbox. I guess that you've enabled "Optimize Mac Storage" in iCloud in System Preferences. If you've done that, only the placeholders of the files remain on your Mac hard drive. That is why the ebooks' record folders are empty.
In fact, to transit files from iCloud to Dropbox, you need to download files locally on your Mac from iCloud storage first. Then, move them to Dropbox. To access the lost ebooks, you can log into iCloud.com to find them.