I think your issue is twofold and by transplanting you can solve both issues at the same time.

Yes, you have to worry about root rot. But your ph being off is more of an issue than root rot you don't have yet. I love a good root product like Cannazym that prevents root rot and Rhizotonic with helps TREAT root rot. Consider one for your plants and growing. I'm wondering if you can add H202 to your flushing but am not really sure in soil so hesitate to tell you to add it. Something to think about though.

If you have done something different to your plants and then see a change for the worse by all means fix it. Remove the stuff and see what happens. Plants do things for a reason.....they don't just decide one day to get root rot or act funny.....they respond to their enviroment. If your roots are coming out the bottom then yes, these things can happen. You can get root rot. Your ph will drop. Your plant will not grow well and becomes at risk for all sorts of diseases, molds etc. If you cant get ahold of larger pots such as 5 gallon and get your girls transplanted in the next day or two (tops!!!) then I'd go ahead and flush with water ph'd to 6.9 until you get your desired runoff. It may take several gallons so I do mine in the bathtub.

Your questions are fine....they are thought out and reflect your willingness to do the work required to grow good plants. It's all a learning thing......but those who teach love to teach to those who listen and learn. I have a feeling you are capable of both.