^ Dude, I have the same problem as you! My HC Cuba grows great but some of it is covered in BGA. Using a suction tubing, it just uproots part of the HC if I'm not careful.
It's interesting to see the HC Cuba's response to an Algae (bacteria) attack, it will send runners and grow new stems while the affect ones melt. What you get is a healthy top stem that floats away from the affected runners.
I haven't tried EM yet, but I can tell you that a black out didn't work for me. The BGA was present in the filter media which is completely void of light. Limiting or increasing fertilizers did nothing but affect the rate of growth of my plants.
This is what I'm going to try to do, maybe you can try this method before tearing this beau of a tank down:
Manual clean of filter media,
New Tubing for Canister filter,
EM or try Kanaplex's Seachem medication
(You might have a strain of BGA resistance to EM)
Daily Bedtime stories to the plants, 1 hour before lights off.