Apple making device migration to Microsoft Intune easy with upcoming OS 26 release

I am experience exactly the same, migration process works great but managed apps are removed (the data also). Intune_Support_Team​ how to enable " Preserving Managed Apps". As documented by Apple:

A device management service has the ability to preserve Managed Apps on iPhone and iPad devices during migration. If an organisation wants users to have the same set of Managed Apps after migration as they had before migration, preserving apps during migration ensures no data loss and a quicker migration because the device doesn’t need to download previously installed Managed Apps.

Managed Apps that install from a package

The operating systems manage apps that install from a device management service differently, depending on whether the Managed flag is set:

• If the flag is set: The app is a Managed App and the operating system removes it, but any extra files outside the /Applications folder remain, for example, a launch agent.
• If the flag isn’t set: The app isn’t considered managed and stays on the device along with any extra files outside the /Applications folder.

Managed Apps that install from a package using declarative device management can specify what to remove in the uninstall script associated with the package, so the device management service removes all items associated with the app.