I gave what you suggested a try, but didn't let it finish. I guess it was tagging stuff but after letting it go 5 hours and it not even processing the stuff in the import folder I figured it was enough. I still didn't even try compact yet but I figure that would have taken even more hours. So I just unsubscribed from the groups and had NB delete all the data. I guess trying to flag 1000 days worth of spam posts in most of these 100+GB groups would do that, but it just wasn't worth keeping around even 200 days worth for the time it was taking.
BTW, I can set the a groups download to be 1 day, but is there a way to set it smaller than a day like say a fraction of a day (like .25 for the last 6 hours)?