Oh God, I'm answering these questions to myself.

Of course it would be bad, because now my roots are in the reservoir, so when I am pouring the nutes into the res they are hitting the roots! Concentrated ProBloom can't be good for roots!

Dammit, I'm an idiot. Why haven't I thought about this? I am going to flush my system and measure out the nutes I need in the 5 gallons so no nasty concentrates are hitting my roots.