I was tucked up in bed, fast asleep when you posted.
No, the re emergence only happens if you stop all abx without either having used flagyl or not taken the other stuff for long enough. You could feasibly eventually rid your body of CPn by never taking flagyl, but you would need to take the other abx for years and years. The minocycline and zithromax you are taking holds the CPn in stasis. It will eventually be flushed out of your system as your own body cells are replaced. This takes a long time.
Daunted is correct about David waiting a minimum of three months before starting the flagyl. He always has waited that long, he did with me, but now, with some people he judges it best to wait up to six months, so don't worry at all that you have missed the boat.