How can I sync my iPad apps onto a new iPhone? I've just got a new iPhone and I want to sync my iPad apps between the iPhone and the iPad.

However when I try to enable synchronization for apps for my iPad, it says that if I try to synchronize, all of my apps will be deleted.



Am I doing something wrong? I understand that I should first synchronize my iPad apps into iTunes and then enable app synchronization for the iPhone ... but I don't want to lose the apps that are installed on the iPad in the process.
No, you're not. The iOS device is a consumption device - every time you toggle the app sync option it will try to "reset"/wipe the existing apps and re-transfer them. Either leave that option on or tweak it and set your sync to Manual. 

To sync your apps to a new device, you have to transfer as to it as a new device. Existing folder structures you had on the iPad do not transfer to phones. You cannot restore configs between different devices.

New phone = new setup of apps and their folders. You sync between your iTunes library and device not device to device.