Select all the photos in Library.
Click the flag on one image, and they will all become unflagged.
I'm in a similar scenario. Just imported my Apple Aperture library with the Lightroom plug-inn. In Aperture I used flags to identify the pictures worth working on. I have a lot of pictures that still need work, but I could easily identify them with flags. After the import however, 44000 of my 46000 pictures are flagged. Any idea what could have gone wrong?
I haven't done any work in Lightroom, so I could easily reimport the aperture library. The import however is a 2 day job. I don't want to spend 2 days to get the same (wrong) result...