That's very weird, Google should have valid reason to remove links from index.

First of all try to ensure that links are really not indexed, because GWT often reports inaccurate stats.

Try to do the search in Google site:www.mysite.com

You will be able to check the real site links added to Google index.

You can also check if a particular link is indexed using the exact link
site:www.mysite.com/article.html

Of course i assume that there are no robots.txt rules or htaccess blocks for Google bots.

Cheers,

John