I select an implant, have the batteries set to "auto" and start doing my thing in PS2. I don't pay a lot of attention to it but after awhile I'll notice the implant is gone. I haven't been able to figure out what makes it disappear (I still have batteries)? I don't think it's dieing (which I'm very good at), maybe spawning vehicles or switching to a max?
You just probably have changed class and haven't placed the implant on that class's implant slot. The implants are like loadouts, they aren't global when you equip them.
And if you did manage to make the implant vanish... that would be a good /bug report if you can figure out how to make it happen again.
It would be just fun flipping fantastic if the game auto-combined implants into chargers for you without asking when you have auto-refil checked on your energy. Everybody loves anti-consumer options.