Index Status Dropping in Webmaster Tools. Permalink settings issue?

WordPress version: 3.5.1.
WordPress SEO version: 1.4.4.

I did this: checked boxes for: Redirect attachment URL’s to parent post URL.
and: Remove the ?replytocom variables.

I expected the plugin to do this: help index status in google webmaster tools

Instead it did this: dropped index status from 1,574 to 1,042 from Feb 24th-March 17th.

My main question is, by redirecting and removing variables, would this cause a drop like this, and would that be positive vs. negative if it was de-indexing duplicate pages?

This is the only change I’ve made to my SEO settings in awhile and then this happened.

I have no idea if a Panda update also affected or if my disabling then re-enabling all my plugins last week after my site broke might have caused the issue?

I follow best practices and avoid duplicate content, so this is concerning me. My pages have been steadily indexing until now.

As far URLS submitted, it looks better, as I have 173 indexed out of 183.

Also, my blog hit the one year mark last week, so I have idea if google cleans house in some form or fashion.

Any advice would be greatly appreciated.

Thanks!

Michael

http://wordpress.org/extend/plugins/wordpress-seo/