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If it's not running it WILL be too high. When it's not running the pump isn't running, and all the oil that is circulating in the trans is hanging out in the pan.
Idling in P or N, depending on the vehicle. Always.
And yes, you are right. Changing extremely dirty fluid (more specifically, flushing it) will almost assuredly cause problem if it's been 80-100k since the last flush.
You should be able to safely drop the pan, put in a new filter, and fill it back up... then you'll have 5ish qts of new fluid and should not have disturbed any sludge deposits
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