I do notice that when searching Rank 40th with mysite minus the extension
My site also recently dropped from page 1 to 4, 5, 6 on hundreds of terms......even the obscure non competitive ones. Pages are not gone; however, they all appear to have big demotions. I have not touched the site for the past week so I doubt your change caused it. My site has been around since 2003, DMOZ listing, good PageRank...yada yada.
site:mysite.com ...my index page shows as the second listing from my site, while all my unaffected competitors show their index as the first listing.
I do notice that when searching
Rank 40th with mysite minus the extension