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I backup my Mac laptop to a volume on an external Thunderbolt drive using SuperDuper. This drive gets removed every day when I take my computer to work, then reattached when I get home. Because it's a clone of my hard drive, I would like to exclude this drive from being indexed by Spotlight, to avoid getting duplicates in my Spotlight search. I have tried adding the drive to the "Prevent Spotlight from searching these locations" list on the Privacy tab of the Spotlight Preference Pane. Unfortunately, MacOS seems to forget this setting every time the drive is removed (every workday, in other words). Is there some way to prevent Spotlight from indexing the drive that will endure even after the drive has been removed an reattached?

Hardware is a Macbook Pro with Retina Display and a Seagate GoFlex Desk Thunderbolt drive. Currently running MacOS 10.7 Lion (at least until the Mountain Lion Up-to-Date Program manages to get itself straightened out) and SuperDuper 2.6.4.

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This ended up being a SuperDuper! problem. It was doing a fresh copy rather than a smart update and when it does that, it sets the drive to be indexed in spotlight rather than retaining your previous setting. Once I set it to smart update the problem was fixed.

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You might want to look at Spotless. I haven't used it personally, but it supposedly fixes the problem you're describing.

http://www.fixamacsoftware.com/software/spot4/index.php

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