Yes, running open circuit is not a good idea for any mill without pitch controlled blades.
In normal operation the open circuit voltage is irrelevant although it could be interesting to measure it below cut in on the motor terminals before the blocking diode, it is interesting to see how far you are from cut in.Beyond cut in you will measure battery volts. Current is what matters, that is the thing to measure. With the mention of consistent high voltages, whooshing noises and no mention of current I was a little worried that you may still have a connection problem.
If these were just voltages taken deliberately on open circuit and not the normal then ok, but it is not good practice and could be very damaging especially with dc motors. Alternators will not bother about a rush of current when you reconnect but the high surge current is not very kind to the brushes and commutator of a dc machine. These motors are pushed very hard for wind power and surges from reconnecting from overspeed are not good.
Flux