Mat, running in sensorless mode should not cause any problems whatsoever, but it does make pulling away on steep hills a bit more difficult as you cannot simply pull away from a standstill with motor assistance.
I ran mine in sensorless mode for several weeks until I finally got around to replacing the blown hall sensors. Although I found it to be marginally noisier than running in sensor controlled mode, it still ran smoothly all the way to maximum speed once it had started running.
Your problem could be caused by one or more failed hall sensors, or a poor connection on the hall sensor wiring.
The external connections should be easy enough to check, but the internal ones will obviously involve removing and dismantling the wheel again.
Alan