Many enterprise customers migrate from Configuration Manager to Intune through long, phased projects.
Applications often stay co-managed in both environments for extended periods of time.
For some internal or sensitive applications, customers are uncomfortable with migration steps that involve cloud handling, such as:
Installer files being uploaded to cloud storage
App content being scanned or processed outside the on‑premises environment
No clear way to keep specific app content fully customer‑controlled
Because of this, customers may avoid using migration tools for these applications, even when they are otherwise committed to Intune.
Why this matters
Without a secure option to keep sensitive app content local:
Some applications must be excluded from migration
Migration projects become incomplete
Intune adoption may be delayed due to security concerns
Providing a customer‑controlled option for sensitive apps would help organizations migrate more confidently and fully.