No one has said it's bad, just that it's unnecessary. That line is only intended to backfill the crankcase with fresh air. The flow direction is in, not out.. Just to educate myself, why is it bad to have a CC on the clean side? Does it hurt anything if it's only connecting the valve covers to the intake?
Are you running ethanol?The CC did have a lot of gunk in it when I dumped it. Slimy water that smelt like gas.
To be safe, I think your best course of action at this point would be plumbing your CC between the valley and snout, and then restoring the lines between the intake tube and valve covers.