Update from iOS 4 to 6. Do I have to sync apps?

I'm helping out someone with updating his iPhone from iOS 4 to 6. I synchronized his iPhone with my laptop (only music, so no apps). Now if want to update it says that all apps will be deleted while updating, so I have to update using the same computer as I synchronized it with.
Because I did not synchronize his apps with my laptop I am worried that he will loose his apps when I do synchronize. But I do not want to synchronize his apps with my laptop because that will mess up my apps (right?).
Does anyone know if I can update to iOS 6 without synchronizing his apps with my laptop?

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