Another possibility for congregating at the inflow is that is what fish that are stressed do. Many times disease problems reduce their ability to uptake oxygen so they look for areas of increased oxygen.
My guess is this will run it's course and most of your fish will survive, but it may reoccur at the same time of year next year or it may not.
I would be interested in your D.O. readings, but if it wasn't for your brookies being just fine, my WAG would have been your dye has cut off light from macrophytes and algae. This could have caused them to die and D.O. readings to plummet. But seeing that the brookies don't seem to be effected that does not seem to be the case.
