How do I reset the thumbnail cache?

Thumbnails are stored in ~/.cache/thumbnails. Simply deleting everything in there will reset your thumbnails, causing them to be recreated according to the global settings. I'm afraid I can't think of a way to prevent a specific directory from being thumbnailed.

Note: In Ubuntu 12.04 (Precise Pangolin) and older, the thumbnails are stored in ~/.thumbnails. But please verify this for your own distro. Lubuntu 12.10 (a clean install) has its thumbnails in ~/.thumbnails and there is no thumbnails subfolder in ~/.cache.

BleachBit can wipe your thumbnail cache, I believe. Not sure how to blacklist a folder from getting thumbnails, though.