I can clear the SQL table by going into the PIM Sync Options of the user and setting "Automatic BlackBerry Device Management Enabled" to False, clicking OK, waiting 1 minute, then going back in and setting it to True.
BlackBerry Enterprise Server on Domino Discussion: Software Configuration Push Problems Wrapup
I noticed however that the single row that gets added after resetting to true contains the old version of the app, with a Status of zero (Upgrade Required?)
Then when I Assign Software Configuration the extra row gets added with the new version.
It seems like that device is stuffed, as each time I clear the tables BES ends up adding rows for the old, then the new versions.
Please don't tell me I have to do an Enterprise Activation, doing this for even a small portion of 2000 users will be painful