Will Ipad 3 delete my photos?

I initially transferred edited pics from my PC to the Ipad via Itunes. However, it seems that if the photos are moved or deleted from the PC harddrive the pics are deleted from the Ipad when synched.  Definitely, not what I want. I switched to using a camera/card adapter and renaming the edited files so the Ipad would think they were from a camera. Minor nuisance. I use the PhotoMngPro app to organize the photos. Good app. I would like to upgrade to IOS 6 from 5, and think I read all my photos that aren't sync via Itunes will be deleted.... not good. No response from the app developer. Any experiences? The Ipad is great, but the Itunes lock down is somewhat frustrating compared to using the Kindle Fire HD, which acts just like a storage device for easy file transfers, etc. Thanks

Greg