And all my pages are indexed in Google after manually checking.

Precisely how did you do this manual checking? A site: search may not reveal the difficulty, and an actual query on Google may be required.

What page do you see returned when you search for your business/site name on Google? If there's text on your index page that is unique to that page, also try searching on Google for that text in quotes.

On Google, if your site doesn't appear for the queries I suggest, are there any other sites being returned for queries like your site name, and for other searches that your index page traditionally "owns"?

Try these same searches on a search engine other than Google.

Complete conjecture, but there are current numerous reports of proxy hijacking, where the hack is cloaked for Googlebot. Via direct navigation, or to the eye, everything might seem normal... but via a query on Google, the site would be replaced by the proxy. Again, a site: search may not reveal the difficulty, if there is one. I have no quick answer for the WordPress stats.

There's a potentially related discussion here, which is what prompts me to consider proxy hijacking as a possibility...

My site's being de-indexed and replaced by others
Feb - Mar 2016
https://www.webmasterworld.com/google/4790240.htm [webmasterworld.com]

By manually checking I mean just putting an entire url address for a page into google search. If the page comes up in search, it is indexed. All my pages come up in google search. Also if I search all the ranking queries they come up as well. All my pages are definitely still indexed in Google for sure. All pages are indexed yet GWT keep dropping pages. Just checked this morning. Almost all pages are showing as no longer indexed and also noticed that almost all backlinks have disappeared as well. Very strange behavior. When I go into the wordpress stats for the site all traffic is the same as it's always been, no change Also shows most of the traffic coming from google. This all makes no sense. Sitemap was not changed, nothing was changes on the website or any GWT settings. Just out of the blue GWT indicates Google dropping all pages, images and backlinks. Really freaky! I read through all the info you mentioned about the hijacking. Don't think that is what's going on. I don't see anything being replaced by others. Not sure. Going to read through it all again. Don't fully understand how that could happen on a secured server. I personally thing GWT is just messing up. Hard to verify anything.

Also meant to add in regards to manually checking for indexed pages. I have searched with the "site:mydomain.com" query and all pages are there. It just seems like Google Webmaster Tools is messed up. Also in regard to backlinks, I have used several backlink tools to check backlinks and all back links show up with 3rd party tools but Google Webmaster Tools showing just about ALL backlinks gone! At present I am trying my best to just totally ignore GWT's results.

Anthony, this has happened to me twice. The indexed page count starts dropping but in actuality those pages are still in the index. IMO it's just a bug in Google'reporting which probably should correct itself in a week or so.

keyplyr + That is what I am thinking/hoping. Hard to ignore but doing my best to not even open up GWT. Just seems to be giving me false information.

Believe me, I was pretty upset... even after finding all my pages accessible in the search index. There's just something powerful about that report.

It was reassuring to read that a couple other people here at WW were also seeing goofy reports in GWT.

The second time it happened, 6 months later, I knew what was happening.

Tnanks keyplyr for jumping in.

(Mod's note: Changed title of thread from
"Google Webmaster Tools Dropping Index Pages"
to...
"Google Webmaster Tools Dropping Indexed Pages"

There is a big difference.)

Thanks for the correction! :-)