I have no idea why that one folder "didn't make the upgrade", never heard of anything like that before. Have you opened the last LR2 backup catalog (using LR2 of course) to verify that folder is still there in the catalog?
Assuming it IS still in the backup catalog, I guess you'd be looking at doing something like this (after making sure you have a backup of your current LR3 'master' catalog):
1. Start LR2 and open that backup catalog. Select the folder in question in the Folders Panel and do "Export as Catalog" to create a temporary catalog containing just that folder (no need to "Include Negatives" during the export, and do not check the '"Include Selected Photos only" option).
2. When the catalog export has finished, close LR2 and then open LR3. Do File>Open Catalog and select the temporary catalog created in step 1. Lightroom should offer to upgrade it, which you accept. It will create an upgraded version of the temporary catalog, make sure you note the name and location. When the upgrade is complete, verify you can still see the folder.
3. When 2 is complete, open your Master catalog in LR3, and then remove the problem folder that you re-imported (right-click on it in the Folders Panel and select "Remove").
4. Then do File>Import from Catalog and select the upgraded temporary catalog that you created in Step 2. This should identify the folder and its contents as import candidates, and you can simply choose to "Add" the files from their current location.
That should work.....though if you're not sure at any stage best stop and get back to us.