Restoring Your iTunes iPhone Backup (and How to Preserve WhatsApp with Intune MDM)

Restoring an iPhone backup can be straightforward — even when the device is managed through Apple DEP / Intune MDM — as long as you follow the correct sequence. This guide covers backing up the old iPhone, preparing the new iPhone, restoring from an encrypted iTunes backup, and preserving recent WhatsApp messages.

Not on Find my Phone...

This feature needs to be disabled on the phone, however I had an issue with being unable to turn this feature off, this needs to be disabled to restore the backup, but when I tried to turn off this feature I got the error:

"Cannot turn off find my iPhone there was a problem removing this iPhone from your account"

I originally though this was to the device restrictions, but upon starting the application I notice that the Wifi I was using was blocked the "Find my iPhone" service as when the application was started I got this error:

When I joined the Wifi that did not block the endpoint then "Find my IPhone" could be disabled as required for the restore, however also remember that if you are using InTune as your MDM then you may also have problem with the following restrictions if applied, these being "Block Find my Friends" and "Block Configuration profile changes"

iTunes access restricted : MDM 

When in this case using InTune as the MDM if you have a USB restriction applied mainly the one shown below called "Block pairing with non-Configurator hosts" enabled as below:

Then when you connect this device to your laptop you will get the error below and iTunes will be unable to see your iPhone (or iOS device) as the configuration above it blocking this access:

When this policy is no longer applied and you connect your iPhone to iTunes when you should get a dialogue like this, where you need to trust the device for it to appear in iTunes, 

Then when you now visit iTunes and plug in your device you will not see it appears in iTunes from here click on the "Summary" then choose under Backups > This Computer > Encrypt Backup > Backup Now

Step 1: Backup the Old iPhone

Before doing anything with the new iPhone, ensure all data on the old iPhone is safely backed up:

• Connect the old iPhone to your computer with iTunes (Windows) or Finder (macOS).
• Select the device and click Back Up Now.
• Enable “Encrypt iPhone Backup” and set a password (This ensures passwords, Wi-Fi settings, Health data, and WhatsApp login sessions are included.)
  
• Wait for the backup to complete.
• Having an encrypted backup is critical for preserving data integrity, including WhatsApp sessions and other app-specific settings.

Step 2: Prepare the New iPhone

Before restoring your iTunes backup, the new iPhone must be properly prepared to ensure DEP/Intune management stays intact and the restore works correctly.

1. Turn on the New iPhone

• Press and hold the power button until the Apple logo appears.
• Wait for the device to boot into the Hello / Setup screen.

2. Connect to Wi-Fi

• Choose your Wi-Fi network.
• Enter the Wi-Fi password and connect.

DEP enrollment and iTunes restore require an internet connection to activate MDM.

3. Complete Initial Setup

• Choose language and region.
• Set up Face ID / Touch ID if prompted (optional — you can skip and configure later).
• Create a device passcode — this is required to continue.

4. Turn Off Find My iPhone

• Go to Settings › [Your Name] › Find My › Find My iPhone.
• Toggle Find My iPhone off.
• Enter your Apple ID password when prompted.
• This step is essential — iTunes will refuse to restore a backup if Find My iPhone is enabled.

5. Complete DEP / Intune Enrollment

• The device will automatically detect your organization’s MDM profile during setup.
• When prompted for Remote Management, tap Enroll.
• Enter any required credentials (usually corporate username/password).
• Wait for the enrollment to complete.

• Verify MDM enrollment:
  

  
  Settings › General › Device Management (or Profiles & Device Management)

• Your organization’s profile should appear and show Supervised / Managed status.

DEP ensures the phone is supervised and policies are applied automatically. Completing enrollment first prevents any conflicts during backup restore.

6. Verify Basic Functionality

• Open Settings › General › About to confirm iOS version.
• Check that the device is connected to Wi-Fi.
• Confirm that Intune management profile is active and policies (Wi-Fi, VPN, email, etc.) are applied.

Step 3: Restore the iTunes Backup to the New iPhone

• Connect the new iPhone to the computer.
• Open iTunes/Finder and select the device.
• Click Restore Backup and select the encrypted backup from the old iPhone.
• Enter the password used with the old phone to restore this backup
• Wait for the restore process to finish and the device to restart.
• Confirm Intune policies are still applied and management remains intact.

At this point, all apps, settings, and WhatsApp (up to the backup date) are restored.

Step 4 : Reverify DEP/Intune Enrollment

When the restore started in iTunes has completed the phone will restart and you will need to re-verify DEP/Intune enrollment - this is required to preserve any applications delivered by Company portal.

Step 4: Preserve Recent WhatsApp Messages

The messages stored in the database for WhatsApp will be from when the backup Was taken this means if you have a couple of days you will be missing messages - This means we need to restore these messages from iiCloud.

Restore WhatsApp from iCloud

• On the old iPhone, verify WhatsApp iCloud backup is up to date, from this tree > WhatsApp › Settings › Chats › Chat Backup
• On the new iPhone, open WhatsApp and sign in with the same phone number.
• WhatsApp will detect the iCloud backup and prompt to restore.
• Confirm to restore messages received after the iTunes backup.

This will overwrite WhatsApp chats from the iTunes backup only; all other data remains from the iTunes restore.

Step 5: Verify Everything

1. Open WhatsApp and confirm all chats, media, and group memberships are present.
2. Confirm the device remains enrolled in Intune and all corporate policies are active.

Step 6 : Check WhatsApp contacts are preserved

When the restore from iCloud to WhatsApp has completed, check your Contacts show the name rather than just a phone number, the encrypted backup should have preserved this data (obviously, this requires you to have encrypted the backups with a password missing the step will result in incomplete data)

If you still have the original phone and the contact data is not there you will need to complete the steps in the article here on the old phone, not the new phone.

Key Points to Remember

• Always back up the old iPhone with an encrypted iTunes backup before restoring.
• Find My iPhone must be off to restore via iTunes.
• Encrypted backups preserve passwords, app data, and WhatsApp sessions.
• Recent WhatsApp messages can be restored from iCloud if necessary.
• Never attempt a full iCloud restore after iTunes restore — it overwrites other app data.

This process ensures that you:

• Preserve all system and app data from iTunes
• Keep DEP / Intune management intact
• Safely recover any recent WhatsApp messages