I have bought a number of apps on my iPhone. When I try to set up syncing with iTunes it says that this will remove all of the apps.
How do I make iTunes not want to replace all of the apps and instead just make a backup of the existing ones?
I had this same issue after I recreated my iTunes library. This may be totally off because it was about a month ago, but I think I did this:
Sorry this is so vague, it's been awhile :)
I just tested this out by alt clicking iTunes, creating a new library, and connecting my iPod. It's pretty much exactly how I described.
Afterwards, you can sync, and everything will be erased and rewritten to the iPod.
I'm not sure why Apple makes this so confusing. The only reason I can come up with is that they want people to have to repurchase stuff but that seems a little over the top even from Apple.
When you plug your iPhone into your computer and sync it with iTunes, it will first copy purchased apps to iTunes (it shows this on the status window), then complete the sync.
I purchase apps on my iPhone/iPad all the time and don't worry about it, just plug in and sync.
I asked the same question on SuperUser a while ago, and nobody could give me a solid answer.
What I ended up having to do is just download all the apps that I wanted in iTunes then sync my iPhone. I cannot remember if iTunes actually removed the apps that I did not already have in iTunes, but in the end it worked.
PS. I hope you don't have too many apps :)