@Zeeshan Bute, Thanks for posting in Q&A. Based as I know, when you directly remove the company portal app on iOS device, the device record still exists in Intune and Microsoft Entra. So when apply conditional access, it still works.
If you want to unenroll the device from Intune, you can remove it in company portal instead of just remove the app.
https://learn.microsoft.com/en-us/mem/intune/user-help/unenroll-your-device-from-intune-ios
Or you can delete the devices from the Intune admin center to unenroll the device from Intune.
Hope the above information can help.
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