It is hard to know if it is the chicken or the egg. On August 5 I upgraded to WP 3.6 from the last revision.
On 8/14 I read that I should go into my google webmaster and tell google not to index my replytocom since I have 3000 indexed.
On 8/19 I got a message from Google telling me my top url lost 78% of its traffic and basically asked what the heck did I do.
I noticed all my top urls took large hits and most them have alot of comments.
I went back to google webmaster and reversed what I did. (I originally had let Google decided.) Now google says they are going to ignore my replytocom on their own
I don't do any black hat seo and basically a blogger. My theme is Thesis which contains a rel=canonical link in each post.
No one over there knows what happened.
Right now my traffic is cut in half. My top urls are not getting any love. I am beside myself because I can't find anyone who knows what to do.
My host has no idea either and thinks it has to do with my WP 3.6 update.