Why are apps purchased on iPhone and iPad being deleted from device when synced?
For some reason when it syncs, it sometimes only remembers the iTunes information and doesn't read the device information. So you may find that after syncing it will deleted apps you'd installed and install apps you'd deleted. It's very annoying. To get around that, I have set my devices to not automatically sync when plugged in. When I do plug them in, I right click the device name, click Transfer Purchases, and after that has been completed then I sync.