Sync question: Will my iAnnotate documents be deleted upon iTunes sync?

Apple technology is still very much a conundrum to me. Basically, on my iPad, I have iAnnotate, and i load powerpoints into it for classes and take notes on those powerpoints. I actually havent connected my iPad to my computer since I set my iPad up because I'm afraid at some point in the sync/update/whatever process, my files will be wiped from my iAnnotate app.
Is there any way that my files would be wiped? What would lead to that happening? On a broader scale, can you explain what it really means to "sync" your device when it's plugged into your computer? I know this is such a novice question, but I'm confused about exactly what syncing does to the content and data on your mobile device when you sync it on your computer. Is it essentially wiping your mobile device (and therefore, the files saved on apps), and replacing it with the versions on your computer? (for example, iAnnotate, but with no saved files)?
Thank you for your help.

JTChal,
My name is Andrew, I'm on Branchfire's Support Team.
Any update - has the potential to cause issues with the data stored in on your iPad.  At Branchfire, we highly recommend user's make use of a cloud-service like Dropbox, Google Drive, Skydrive to store your documents.  That way you always have a backup of your work (and most of those service have methods of recovering previous version and even deleted files).  We provide easy ways to connect to these cloud-services within iAnnotate to easily access your files, annotate them, and ensure they are saved back to the cloud. 
We highly recommend you email our support team at [email protected] if you have further questions - it is the best way to ensure we see your question and get you a helpful response. 

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