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I had a major issue in the last week where a site was found to be showing huge numbers of pages that it shouldn't have been. Naturally Google indexed all of these pages!

Rather than manually remove 5000+ links, I thought the nuclear option of removing the whole site would be the best option (using the Remove URL tool with no URL provided), since the site was poorly ranking anyway.

I had read that this was a good way to reset your site if you wanted to start over.

I removed the site, then after confirming that Google had removed it, I resubmitted the site for indexing and submitted a new site map and a new robots.txt to prevent indexing of the restricted pages.

The sitemap shows that it is indexed (or at least, a large portion of it is indexed) and I can see the Google bot activity on the site.

However, on my dashboard I see severe health problems listed, with the main one being important page removed and a link to the removal request for the main site.

Furthermore, there are no links to the site in the Google index (when tested against site:mysite.com in a search).

Do I need to reinclude the site using the removal tool? If I do this, will it re-add all the bad URLs that I was trying to get rid of?

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How long have you waited? indexing takes a while and one crawl may not mean you get indexed. –  bybe May 13 '13 at 15:59
    
@bybe-- thanks, I know it can take a while to get indexed, but I'm more concerned with the severe health message-- do I just need to wait a while for this to go away? Does it block the indexing of the site? –  user101289 May 13 '13 at 16:08
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2 Answers

The URL removal tool prevents your site from appearing in search results, it doesn't "reset" your site's indexing. To allow your site to appear in search again, you need to cancel the removal request.

In general, if those unnecessary URLs now return 404, then they'll drop out on their own, there's no need to submit URL removal requests for them. It can take some time (sometimes several months), but that's normal.

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thanks John. The question is will all the "illegal" URLs be re-included also? I wasn't quite clear on the initial post-- but these aren't just improper URLs, they are / were / accidentally showing sensitive information. The links have been fixed to not display this info, but searches for the sensitive info will still be returned in the Google index if they are reincluded. –  user101289 May 15 '13 at 16:02
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If you cancel a site removal request, "everything" will be visible as it's indexed, assuming it's not individually removed as well. If the content there shouldn't be indexed, I'd try to submit these individual URL removal requests first, and then cancel the site removal request. For natural changes on sites, I'd just let them drop out naturally, but if it's really problematic content, being extra-sure that they're removed might be a reasonable strategy :). –  John Mueller Jun 13 '13 at 13:28
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Do I need to "reinclude" the site using the removal tool?

You can't "reinclude" the site using the removal tool?! It is a removal tool. Although it seems you can "undo" (ie. re-include the URLs) by canceling the removal request. However, the docs, suggest that "your content may later reappear in search results" regardless of this action.

You generally "include" a site by submitting a sitemap and generally making the site crawlable - which you seem to have done.

on my dashboard I see "severe health problems" listed, with the main one being "important page removed" and a link to the removal request for the main site. ... I'm more concerned with the severe health message

The "severe health message" is most probably because your site has been removed from search - that is pretty severe! It is informing you about a past event, it is not necessarily current. You can have more than 1 admin/user in GWT. If a rogue admin should "remove an entire site" then the messaging system ensures the other admins are informed and can take action.

As bybe and yourself suggest, it will take time...

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Hi-- thanks for your time. However, yes, you can re-include items you've removed in the URL removal tool. Once a removal request is accepted and completed, you can filter removal requests by "Removed"-- then you'll see the completed request along with a button saying "Reinclude" –  user101289 May 14 '13 at 15:10
    
Ah, thanks for the correction / feedback! I assume this is to correct/undo a mistake - it would not normally be required in order to reindex a site. Unless you can selectively "re-include" URLs, then as you suggest, it seems likely that it would re-include the bad URLs as well. –  w3d May 14 '13 at 18:26
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