Revert to 3.1.1 (Permalink Problem)

Anyone have any ideas how to revert to an older version of wordpress? I recently updated my network (of about 1200 sites) to 3.1.2 and it broke the permalinks on the the main site (but none of the sub-sites).

It appears to be the problem described here:

But the resolution does not work. I have tried working with the .htaccess file, activating the plugin, nothing seems to work.

So, I want to revert to 3.1.1 until wordpress addresses this bug. I tried just manually uploading the 3.1.1 files, but all the sub-sites (and the main site) still say 3.1.2 in the footer. I tried doing an network update again, but that didn't seem to work. Any ideas?

Or even better, some other ideas how to fix the permalink issue.

Thanks so much!