Now using the Magisk Manager download the Magisk-v12.0.zip archive and install it via TWRP Custom Recovery.
In Magisk settings enable “Magisk Hide” and disable “Turn on BusyBox”.
To hide root from some apps, open “Magisk Manager” > Go to “Magisk Hide” and select required applications.
If this method didn’t worked, then try to download and install Xiaomi SafetyNet Fix via TWRP Custom Recovery. Also you can try installing another version of SafetyNet Fix module, this is version for Mi5, but will also work on Redmi Note 3 Pro.
Now, if the SafetyNet verification passes successfully, but some applications are still getting blocked, then may be changes to “build.prop” could help. You may try changing the parameter “ro.build.tags”. Change the value from “test-keys” to “release-keys”.