There must be something in your well water that is feeding a biological growth in the reservoir. Of course you can deal with reservoir by using some peroxide, but this will kill off the microbes in the roots as well.
If you choose to go the RO route. The low numbers of the well water will mean a long life of the individual filter cartridges. I have never replaced the filter cartridges, and still getting an EC off .002.
I’ve done some reading and it sounds like sulfur bacteria. When I filled the tanks there’s no smell but after a day it starts to smell mildly eggy. Not terrible but I’m assuming that’s why my ph jumps big values. And it’s not just one day I ph back down it’s like every 12 hrs it goes from 6.0ish to 7.6ph in the Rez and the trays are almost 8. That’s why I thought the mimosa was droopy because of ph. I’m hoping a RO system will rectify this. I have a plain bucket with water and I’m testing and writing down my finds to see if the wave maker creating heat or movement is the problem. I also have a tank that injects chlorine and acid into the system for smell but the pump is acting up and I didn’t want those chemicals in the soil either. I did hear of the peroxide but didn’t want to ruin all the good bacteria’s in the soil. Even my neighbors well water was 160ppm mine is much less. I’ll probably order the buddy today. I don’t want to have ph issues in flower like my last grow.
I’ve been using auto pots for about 3 years now, the old and new systems. Wave makers help with the drift, I started mixing 2-4 gallons in the res to help mitigate the upward PH drift 
So you’re saying you add more water to the tanks to slow the drift upwards? Is that with nutrients or just plain water? Then I should always use the wave maker? Do you let your water sit for a while before introducing to the trays?
How did you set up your pots? Did you use hydroton in the bottom two inches? Is there a root protector in the pot? The clay balls are there to attenuate the rate of water uptake and could be your one pot is taking up too much and causing issues.
Personally; I use Jack’s and only PH initially when mixing for the reservoir. I don’t even need to flush. My muni water is 7.0/135 ppm. As low a TDS as your water is I wouldn’t see a need to run R/O.
AutoPot now has a plastic base that goes in the bottom of the pots. You pack the little stand pipes with coco, and then sit in the pot on top of the root control disk. It kinda takes the guesswork out how much stones or such that goes in the bottom. The base can be used with or without the air domes.
I top the feed the plants for 2 weeks after the seedling transplant before turning on the auto system and mix the nutrients at a rate of 4-6 gallons sometimes 2 gallons depending on the growth stage as in early veg and late flowering stages where their appetite is low. I’ve never experienced more than a .5 drift. I PH at 5.8-6.0 and it may drift upwards to 6.5ish
@Myfriendis410 you gave me great advice on my last run! yes I did use the airbase with the airdomes. No hydro. I also used the root control discs as well. I was going to switch to jacks after I use up the cronk nutrients. But I still can’t tell if the one plant is overwatered or under watered. The leaves feel papery and limp compared to the others which makes me think underwatered? I really haven’t got a clue. I’ve let them sit now for 2 days and the others still look great. I’m afraid to overwater if it’s not an underwatering issue. I thought maybe RO water would stop the ph from going so high all the time. It’s not even 24 hr it’s like 12 he’s it jumps like crazy.
I think I turned the tanks on at the 15 day mark. They were quite large and I could tell after a few days they took a lot of water. Then I noticed the bubbles at the aqua valve and the one plant looking droopy so I decided to take everything out and give a good clean. Was going to end up doing that at some point anyway for recharge and or fish sht. But my drift goes from 6.1 to over 7 in less than 24hrs. Very confusing. I also didn’t expect them to drink so much water this early. Last run was hand watering and I waited until the fabrics were really light and dry. Your doesn’t drift as much as mine. Maybe it’s the organic nutes? But when it was plain water (coco loco has nutes for maybe 3 weeks?) ph still went crazy. Even recalibrated the apera tester twice.
Is your wave maker running continuously? I found that running short term works best. I had same issue with continuous running. Now i set up a different timer to mix for only ten minutes b4 the feed. Fixed my problem. Still get a drift bit maybe .15 updrift daily. That i can handle. Not a autopot guy but run a res. I know you cant control the valve and mixing time but would reduce the mixing.
The droopy look to me looks like a overwatered symptom. Underwatered the leaf will sag WITH the stem, overwatered the stem is straight and leaf itself is saggy. Hope this helps.
I’ll try that. I do have timers somewhere in the garage.
Well damn. I just watered with nutes and recharge because I figured after 2.5 days she didn’t perk up must be underwatered… Looks like I drowned her…
Pure water will adopt the PH of whatever medium it’s introduced to. The more solids in the water, the more it will resist PH changes as there is more potential hydrogen. Your base water is under 100 ppm so that will easily be moved to the media’s PH. Mine at 130 is close enough I don’t worry about it.
I’ve been doing Autopots with fabric pots and have been more happy with the system. I do appear to get a boost of veg growth and I’ve been getting around 12 oz. of dried flower per plant. 2" of hydroton, no root control discs and coco/perlite.
I think likely that plant has a root issue which could have happened by overwatering at an earlier stage of growth. When you harvest, do an ‘autopsy’ on the root mass: I think you’ll find sparse roots.
If you mix a nutrient solution at, say, 450 ppm and PH it; PH will rise fairly quickly compared to a nutrient solution of 900 ppm. I have no experience with the nutrient line you are using.
Root issue is concerning. If I remember correctly I think I only watered them twice in the 15 days before the tanks were turned on. Then they got plain water in the trays for less than 10 days. Im at day 26 from seed. They really didn’t show growth until the second day they were in the trays then boom they looked really healthy. Your post is very informative and I’ll be reverting back to it to make sure I’m still on the right track. I too got the same yields last run in fabric pots. Hand watered. I have fabrics for the AP system but humidity in late flower was a pain. I’m kinda afraid to keep using the AP setup if it causing root issues…
update
Thank you all for the comments and sharing advice, this is why I love ilgm. I get a ton of knowledge and i appreciate every comment.
I ended up hand watering @6.1 ph 1.3 EC with recharge and fish sht. She took about 8 hrs and bounced right back. Somehow she wasn’t getting water? Find that odd since the pot literally sits in water. I have taken them out and put back in maybe air bubble caught in between? Not sure if that’s a thing. Again I thank everyone who commented and always appreciate the help.
gotta love when the issues can be fixed just as easily as they can be caused
Im glad you fixed the issue, from your posts i can see you are very concerned about tge ph of the water, i use auto pots and mine are a little different than yours i got the black bases 9 or 13 gallon any ways… just wanted to tell ya a few tips from my experience.
Dont check the ph in the tray, it will only fuck up your day lol. Also try a boogie brew filter they are on amazon, ive tried RO did nothing but cause micro nutrient deficiency for me i much prefer filtered city/well water now, unless you got something real funky with your water
Let the water sit out for a couple days or evdn better bubble it, this will help stabilize the waters ph (a little)
Clean your resavoir every couple weeks just soap and water (every week for me i add supplements to my res and need to clean)
Keep the res between 5.8 and 6.4 ish and you shouldnt have any problem regarding ph, however if you do then its likely a problem with the soil at that point…
In other words just make sure its good water and ph correct and you really dont need to worry about flushing the lines or what ph the tray is etc
Hope this helps so you dont stress so much
Also the air lines in my experience are a waste of time and effort 
Yea I’ve now been letting the water sit for a day before I turn on the system. Very good info. Much appreciated. There’s a lot of back and fourth about the airdomes but I figured since i had them I’d try it. Maybe not next time. Haven’t gotten any info if they absolutely work. I’ve also not used the wave maker as much. Seems to help with ph drift. Thanks @GrownInMN!