If no-one else has any suggestions:
You can download the appropriate
Recovery .img file from here.
Boot into it from Fastboot.
Clear Dalvik, cache, and delete the
/data/system/package_cache folder.
Then Reboot to system.
If that doesn't work, boot back into Recovery
Clear process again
Install whichever ROM you want to go with.
Reboot to system.
If that doesn't work, boot back into Recovery
Clear process again
Install whichever ROM you want
Do a Factory reset (clearly you will lose your data here).
Reboot to system
I hope that at least one will work. But someone may have specific instructions for the Mi 9 SE.