So at it's core, Vibrant is 95% bacteria. Theoretically, you really should be able to run the scrubber while you're dosing vibrant. The scrubber provides the ideal place for algae, a lot better than in your tank. I don't know if Vibrant would totally inhibit the scrubber growth, but I would think that it would not decimate it. But, not having tried it and not really hearing from anyone that has, I would think that worst case you would dial back the intensity of the scrubber during treatment so that you don't cause photosaturation.
I don't want to get into a debate about Vibrant and how it works,
there's a whole thread for that. I also don't want to try and counter any claims - honestly, I only know bits and pieces about the product, but if it is mainly bacteria, my logical brain would say the added bacteria via Vibrant are outcompeting the algae for nutrients somehow. Take away the bacteria, take away the competition. Seems like the core issue in either case is the nutrient source possibly?
So then - questions:
How old is your tank?
How old is your rock?
Have you ever had a period of really high nutrients?
How was the scrubber growing when you took it offline?
Why did you take the scrubber offline (guessing, tank algae didn't appear to be affected?)
When did the outbreak start, originally?
Might have more questions.