I think you can exclude the battery brownout. Since the same battery feeds both motors, you would feel the loss of power on both sides.
If you are confident that your power connections (battery to ESC, and ESC to motor) are solid, this leaves a timer-to-ESC connection. If that connection was lost momentarily, the ESC would lose logic power and reset. And even if the 5V and timer signal got restored in flight, the ESC would not resume its operation without going through the initialization sequence from the timer.
Depending on the ESC you are using, it may do something on the output during the initialization process that would prevent the prop from freewheeling for a few seconds.
That is the most likely scenario, in my opinion.
While tedious, there is a way to disassemble those 3-pin connectors and give each sleeve a gentle squeeze to ensure better contact with the male pins.