The trailer brakes are a completely different circuit from the one that charges the trailer battery in normal operation. Now if you have a problem and the breakaway switch for your trailer brakes is pulled, then you must have the trailer battery charged and hooked up to have the brakes applied in emergency situations.
Have you searched for a diagram of trailer plug wiring to check for voltage? If not, search for trailer plug wiring so you will know what terminal to check.
Jim M