I too was having this problem and was quite angry about it. I recently deleted the Evernote app on both my iPad and phone and then reinstalled. When I went to select my off-line notebooks I was able to synchronize my entire database in a single six hour session! This has never happened before, in previous times it took days. Nice to know things are moving forward…
ps- Like Pink Elephant said, in order to get all of your off-line notebooks to sync you need to turn off auto lock, plug in your device and keep the Evernote app open for the entire time.