tdgeek: IMO this thread while helpful I hope to you, it has got confusing. Talk of using the transfer purchases function, connecting the device then stopping the sync. That is all wrong. That is not how you need to manage iTunes and the devices.
When I am home I can itemise my sync settings if that is of help. All I do is connect my device and run a sync from time to time to keep iTunes in line with my device as I add apps on the device. Or to add music, video, pdf files to my device from iTunes.
after hitting yes to transfer purchases i didnt touch anything and waited ... all it did was delete all my apps and then stalled (waited for it to do something but the circle kept spinning and nothing happened for one hour)
bug or user error?