It sounds like your soup was too hot and started to cause lockout. As a rule I follow, I always use RO water so I know exactly where "zero" is. It gets a little tougher to troubleshoot when tap water is involved as everyones is different. RO is RO is RO all across the board. Tap water is the bane of RDWC growing and will always have problems with consistency in your grow. 5.5 to 6.1 is a normal PH swing for any UC system so that's normal. However your plants are using the nutrients in the water. pH going up is a good thing. Bump up those ppms by 100-200 PPM per day and you should start to see your pH level off. If it starts trending the other way, going down, then your ppms are too high. The plants would be consuming water faster than the nutrients. When I dump my soup I leave NOTHING in the system. I mean nothing. I get in there with a shop vac and get all the old soup out. But yes, I PH/
CalMag treat my water and give it sufficient time to degass before I add my nutes then balance it out again. I have been doing something new lately and I am not sure how it will turn out but I will rinse the root masses with ph's water and fill the system before I place them back in the buckets. I want to see if removing the residual salts in the root mass will help the plants with nutrient uptake.