Featured Battery light and continuous beep

I read your long run on sentence for a few times, and I'm still not really understanding the sequence of what you're experiencing and how the car is behaving. And especially strange that the car goes back to normal without any intervention

1. I have an 06 Prius hybrid I fixed the hybrid battery and car runs good for a few miles
2. then charging meter shows nothing in the car powered down you have to pull over
3. restart it and it’ll goLess than a mile in the red light
4. the beep comes back on

So I'm not exactly sure what to make of those 4

 

AND.....exactly how did you "fix" the hybrid battery ?
While you were doing that, did you test the 12 V battery too ??

 

Congrats on taking on a steep learning curve... Did you replace a bad module? How did you test the modules? Have you deep cycled the modules/reconditioned them 3 times?

And what are the error codes? IF you have warning lights you have error codes and subcodes pointing to the exact problem... Dr. Prius app is good for that. Here's a buyer's guide for device you'll need: Hybrid battery diagnostic and repair tool for Toyota and Lexus

 

You have to read codes. A problem that goes away when the car sits would usually mean an overheat condition, like a bad inverter pump

 

Maybe it is more like this:

2. then the charging meter shows nothing in the car powered down.
3. You have to pull over, restart it, and it’ll go.
4. Less than a mile in, the red light and the beep comes back on.
5. After the car sits for a while, it goes back to normal when you start it.

The beep could indicate a very serious problem with the brake system