Well flushing is the right way to go. At 3 weeks old your plants were not ready for full strength nutes. Go half nutes or a little less than half when you add the nutes.

PH is a daily thing. Keep on it at the same time each day it will level out and not change as much. Good idea to change from tap water to R/O, it may have been what was burning them up.

As far as the PPM's. The only way they will change is if your plants are drinking alot of water and I don't think those little ones are doing that.

If your water was low and you added more tap water then it would go up by how much ppm's the tap water has.

If your plants drink alot in a day then PPM's go way up. You add just PH'ed R/O water and ppm's come bcak down to where you had them. Do not add water with nutes only plain water.