keep iPhone-deleted apps on iTunes

The apps not appearing in iTunes is a bug that many users are experiencing. You can try restarting your computer and resetting your iPhone, but it rarely helps.

This is just a display bug and has no effect on the actual apps.

You do not need to remove apps from your phone, in order to then add them to your new phone. All you need to do is backup your current phone to iTunes (encrypted) and iCloud, then Restore that backup onto your new phone. You also need to import onto your computer, your photos, videos and should sync your device with iTunes.

Restore your device from an iCloud or iTunes backup - Apple Support

Apps no longer transfer from iDevices to iTunes.

You need to download them directly in iTunes Store to iTunes.

New "App Thinning" with iOS9: To make apps smaller they are being customized for specific hardware when downloaded from Apple directly over-the-air to a device with iOS9. Apps downloaded directly to a device from Apple may no longer work on any other kind of device. Apple has decided there is no point in syncing these to a computer since each device should ideally get a customized version directly from Apple. If you want a backup copy on your computer you can transfer a non-thinned version directly from the Store to the computer which should you need it can be transferred to any i-device (but will take up more room). You may wish to enable automatic downloads on your computer so there will be a copy of all apps there as sometimes apps are removed from the Store: Turn on Automatic Downloads - https://support.apple.com/en-us/HT202180#computer Extra tips from sberman: Make sure "Apps" is checked. Also make sure the Apple ID shown just below "Automatic Downloads" is the same one you're using on the iPhone. - https://discussions.apple.com/thread/7488774?answerId=29896877022#29896877022

Here's the technical description: https://developer.apple.com/library/watchos/documentation/IDEs/Conceptual/AppDis tributionGuide/AppThinning/AppThinning.html - iOS9 App Thinning > "Slicing is the process of creating and delivering variants of the app bundle for different target devices. A variant contains only the executable architecture and resources that are needed for the target device." ... "The App Store will create and deliver different variants based on the devices your app supports."

Your data is another matter. That should be transferred as part of a backup. It is the apps themselves that are no longer transferred.