New iPhone on account

We used backup to transfer from  a pair of iPhones 4 to iPhones 6.
Not everything came over, so I have had to manually add many things.
Not the apps I paid  to upgrade, not the identities in travel apps, subscriptions, etc.
I have manually added most.
This took quite a while, and a few phone calls
How do I claim the app upgrades I've paid for w/o wiping my efforts?.
How do I remove the old iPhone 4 from the account so "find my friends" will work again?

When you restored from the backup, the phone also needed to sync music and apps, as they are not included in the backup. It is assumed they reside in your iTunes library. The application data is included in the backup. If when you restored the new phones from the old phone backups, you did not wait for the devices to sync, then just go back and sync from your iTunes. That will restore your applications. Then go to  the App Store to check to see if their are updates to the particular apps you are referring to.
In answer to your second question about removing the old iPhone 4 from the account, see this support document that describes the instructions to take to prepare a device for sale or giveaway. That includes removing it from your iCloud account. What to do before selling or giving away your iPhone, iPad, or iPod touch - Apple Support

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