The higher voltage is useful in keeping the wire size down and compensating for voltage drop. If for example the blower was closer to the distribution and now in the loft has moved a further distance from the panel then you might have a few new issues. Starting the blower will be harder and may pull the voltage quite low. If the run current for the motor is over or near the max for the wire size you could also be running into low voltage problems caused by those variables. You could shorten the motor life by running at a constant undervoltage. On the other side the motor may now be oversized as the air column may have lower air resistance.
Now that the organ loft has only the one source to feed the organ I guess the branch circuit is now useless for choir lights or any other 120 volt need since it will be fully loaded when the organ is running.
Maybe the better choice is to run the 220 volt circuit and maybe the person responsible for the renovation may become the wiser.
