Planted Tank Guru
Join Date: Jun 2004
Location: Baton Rouge, LA
Wow, I just saw this thread for the first time. Amazing! Sorry to hear it's not doing well now.
I've had my Marimo balls invaded by various algae a few times. This is easy to treat. In their native habitat, they can survive months without light, during winter when the water is iced over. So I put them in a bucket of water in the closest for a week or two. The Marimo doesn't mind at all, and the invasive algae dies.
I've also had the long, invasive clado in java moss. This too was easy to treat, by moving it to a bucket with AlgaeFix for three days.
But your case is an odd one. All chemical treatments are completely out of the question, leaving only the option of blackout. But I have no idea what the blackout tolerance of invasive clado is. Or if your blanketing clado is the same as Marimo ball clado, and has the same tolerance. It's even possible there's only one type of clado present in your tank, and that it's changing form as a natural part of its life cycle.
I would experimentally remove a chunk of it, with both the desirable and undesirable form/species, to a bucket for a one-week blackout. Then return it to the tank, wait another week, and see what happens.