Web-downloaded epub files won't transfer from iBooks to iTunes

Hi!
Yesterday, on my iPad, I downloaded two epub files from a website (using Safari) and opened them directly in iBooks. They work fine, show up in my Library with no problem. However, I can't get them to sync down to iTunes. This is definitely not the first time I've downloaded directly to iBooks from an app on the iPad (although maybe a first for an epub from Safari?), but this is the first time I've had issues syncing down to iTunes.
I've synced and resynced and resynced and they won't transfer; not only do they not transfer, but if I open the Books folder on the iPad when it's mounted in iTunes, they're not listed. I could put them on my laptop first and then load them into iTunes and to the iPad from there, but I've highlighted and bookmarked in both books and don't want to lose all of that if it's avoidable.
Any ideas? I'm wondering if there's some limitation of iBooks that I don't know. And if there is, is there a way to now get the epub files out of iBooks some other way? (To maintain bookmarks/highlighting.)
Anyway, thanks in advance
P.S. As a test, I just did the same thing on my iPhone with the same results: file won't sync down and doesn't show up when I browse the phone in iTunes.

i have the exact problem last week when I signed up to receive a free epub in the email.
When the email arrived I proceed to open it in ibook on my iphone and started reading, after 2 chapters I decided to sync the phone with my computer and found that it won't sync the newly downloaded epub, not even showing it in the device list in itunes.
So I tried the same thing on my ipad, download to ibook, sync with computer. Same result: the book was not synced and won't show in ipad's book folder in the device list.
Still haven't found a solution

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