It seems to make more sense to me to vacume the stuff up at the brush than to have to suck it through the whole house!
You will be glad you did it though.
I removed some old ducts in a house about the same age, there was about two inches of dust hanging from them.
You should ask your HVAC person to install a allergy type filter on your system. I did in my old house and the dust was cut down conciderably.
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