New update deleted all of my lecture notes and wouldn't restore recent backup. How can I download them from the cloud to my iPad? (not at my computer right now)

Question

(It's fifteen minutes before class starts)
I tried to back up all of my devices before making the update to 7.0.6.
My iPad was ejected and iTunes told me that it couldn't be updated due to some error (this was yesterday). Then when I plugged it back in, it said I needed to restore my iPad, and I couldn't get to the home screen or anything, it just showed a "Connect to iTunes" icon. So it restored a really early version (with notes from last semester but not from this semester), even though I'm sure I've backed it up at least twice since I got it (1-13-14).
I got onto the Cloud and downloaded some important lecture notes before performing the update just to make sure that they would all be up to date, but those are on my computer, which I am currently not at, so I can't download them. I saw that my iPad was syncing with my Cloud, so my college notes were all showing up, and I didn't stick around to make sure that the current ones showed up (but they're on my cloud, so wouldn't they?).
Also, I use Branchfire's iAnnotate PDF, and all of my highlighted articles for research papers and summaries are gone. I'm missing important articles that had notes for two seminars, and they're all gone. I'm confident I can recover things from the cloud, but iAnnotate doesn't use the cloud. Is there a way to find those again?
What I'm curious about right now is if there's a way to download from the Cloud to my iPad, because that's where my notes are.
Does the cloud sync FROM my iPad? As in, if it isn't on my iPad will it delete documents from my Cloud? Or if it's in the Cloud, will it sync to my iPad if it's absent here?
This is really frustrating, especially because I TRIED to back everything up just to be safe. I tried everything, and I still lost all of my important files. This is beyond frustrating, it's devastating. This is unacceptable.

Answer 1

There are some recovery programs out there if you google them - many with free trials. I haven't tried them so I have no opinion.Read any professional tech and user reviews you can find before you try one. I have read here in the past that some have worked for people who have posted here. 
To help in the future, have you considered using Jump Desktop - Remote Desktop? I know it won't solve the problem you're dealing with now (unless notes were taken on your computer.) It's in the app store. It's the #1 paid app in the business category and the reviews are great. It allows you to see anything that's on your computer on your ipad. If you take your notes on your ipad then you might want to email them to yourself, put them on Word in your computer, for example, and then if you need them in class, you remotely connect your ipad to your computer and you will see your notes. This way you won't have to rely so much on the cloud. The explanation would be too long here, but you might want to take a look at it. You can use the free trial on jumpdesk.com and then if it works for you, buy it in the app store. 
Meanwhile, it's hours since you sent this post. Hopefully others who can help solve your problem who are on this forum now can help you. I hope you get your notes back. Don't give up too quickly.
Hope this helps.