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7020100
(Get the code!)
Regarding a mechanism to properly migrate users-settings without hacking new stuff into compiz:
There are several packages that trigger a notification that asks the user to do stuff. ecryptfs asks the users to write down their passphrases, dropbox asks them to restart nautilus.
What about adding that kind of notification just to this particular update telling the user that some compiz settings have to be reset to their default value. There could be a button that runs a script which does a recursive-unset on the relevant keys. I'm pretty sure these notifications work on a per-user basis, so that multiple users on a system will all get the message to run the script.