I just read that I need to remove disallow for all the pages I don't want indexed, wait until they disappear from search results, then add them back. Can I request that they are removed or do I need to wait for it to naturally happen? Do I remove them from the sitemap once they disappear? This is counterintuitive but maybe it is the answer to one of my problems.




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Add new content & ping google.

Also what did you change ?!
I mean if google founded something fishy....

Have you configured webmasters tools?

We cant fix this problem, the reason is Google will changed the algorithm recently.. so that it will happen like this. I'm also analyzed this issues. (we are only thing this is issues, but this is not a issues. because this is current Google algorithm). this same problem happen to my targeted keywords. suddenly my all keywords are going down. now for those keywords optimizing & working in inner pages.

You could check in Google Webmaster tools if something changed, that is if you have it set up from before this happened.
Also it is possible that your inner page is better for some reason, did you changed anything to your home page or used a different SEO method that you have not used before?

Check webmaster tools/robots.txt/meta robots and see if it has been set to noindex/nofollow.

check backlinks you have build for home page because Google implement new algo so may be that's the reason.

Update the content.