You said the air handler is in the attic, right? When you're there, look to see if there's a damper before or after the fan and try to observe it when the system shuts down. You might be able to see the end of the damper shaft coming through the duct. Very possible it's the source of noise. If you have separate zone ducts instead, there may be dampers there to balance the system through I wouldn't expect these to be noisy as they might be motor controlled.
If the noise only happens when the furnace shuts down normally, I don't think it would have anything to do with the filter.
Good luck
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Bob F
Amherst till the big 66 comes (made it!)
Winter Harbor/Mirror Lake till the big guy comes
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