The bee vacuum cleaner sounds a bit brutal if it causes that many casualties.
Often one is able to drive bees from their comb to the container of one's
choice by setting up a vibration.  The technique is to smoke the colony
lightly from below.  Place a shaded skep or new hive above the colony making
sure it is smoke free, dark and that the bees have a bridge to walk up into
it.  Start drumming with your hands on the hive/box/skep/branch containing the
colony at a pace similar to your pulse beat if you're not too excited.  Don't
be too energetic - you may need to keep going for half an hour.  The bees will
peaceably move upwards into the skep enabling you to remove the comb without
interference.  You can treat the driven bees as a swarm or re-unite with them
with their brood comb when tied into frames in the way you described.
Chris Slade