This answer may not fit everyone.
You touched on the reason I gave up growing in the retail Waterfarm units. I like to have a fill and drain port in each unit. So I made my own buckets ,took pictures, and here we are.
I adjust when topping off. Everyday your plant drinks a % of the nutrient solution. I will add a bit of PH Up or Down to my top-off solution and fill the bucket to my full mark. I can do this because I know my nutrients and PH adjustment pretty well.
What you can do till you get the hang of your liquid adjustment is, drain and adjust. Drain out your bucket into a clean pail, adjust and put it back in. A small pond pump helps a ton. Remember you don't have to get 100% of your nutrient solution out of your buckets when you change cycle or adjust.
Pond pumps are great for mixing as well.
