Hi, I have an iPad2 and iPhone 4, everytime I sync, i turns my board into a mess, erases ipad apps, adds iphone apps into ipad, change app folders. i'm tired of this, i gave a quick look on iTunes options but nothing helped.
I have an iPhone 4S and an iPad 2 and connect both to iTunes without issue. I use an iMac. I just make sure that apps I do not want on a particular device are NOT checked in iTunes when I sync. Have never had an issue with content being deleted from one or the other.