Interesting
I think, now that the Native card is installed(and assuming the OMNI is connected and lights up with no error messages), I would uninstall Pro Tools AND the HD Driver and reinstall them(If the HDN card is not an available "audio engine" in Pro Tools>setup>Hardware, then I suspect a driver issue first, a hardware issue second). Also, verify that the Digilink asset is actually on your iLok(not simply in your account) as this bit me in the butt with 12.7(you could test this by installing 12.6 because if that does work, then its the Digilink licence that is not acting correctly, for whatever reason).
I assume the splash screen does show the big HD when you open Pro Tools?(if not, then you have deeper iLok licence issues to figure out)