A few months ago I wanted to play PC games with my ps3 controllers so I downloaded a program to do that and days later both of them stopped working. Up until recently I never put the 2 together but can it be possible that the program somehow made it so that my controllers batteries don't work properly?

I did exactly what you did with your ps3 controllers. Downloaded a program and plug them in my pc whenever I feel like using them. It should not have affected the controller batteries at all.

Whenever the ps3 looses track of the controllers, all thats needed is to plug the controllers back to the ps3 with the usb cable for a few seconds and they should be good to go.