There seems to be some progress for most of the HC in the back (elevated) areas. I suspect the front of the tank was a little too muddy/flooded for the HC's to take stronger roots and flourish. The Riccia's seem to have revived itself and I can see new greens growing. Mold was starting to show at the front, which is what prompted me to clean a little and start flooding the tank.
A part from it being fun to actually flood the tank. I now wonder if it was too soon. (~ 2 weeks emersed / dry start)