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I submitted a sitemap with incorrect URLs. After a few days I looked at Webmaster Tools crawl errors and I saw 1000's of URLs with not found errors.

So I went and fixed the problem with the URLs and resubmitted the sitemap.

The problem is that Webmaster Tools is still showing me the same old not found errors.

1) I know that the URLs in the updated sitemap are ok

2) I can see that the date of the not found error URLs corresponds to when the problem was.

Now I tried using the "mark as fixed button" - but that only lets me select the first 1000 URLs, and then it shows an empty list.... and I have about 40,000 not found URL errors.

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Yes Google shows only top 1000 errors. It will show you the next 1000 errors in next 24 hours. Keep checking every day and click on fixed. I faced similar problem few months back. But I had only 3000 errors so I was able to fix in 3 days.

As long as you don't get any new errors recorded Google will not penalize you.

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    Yeh, that looks right. It's a bit of a pain though that it's going to take 40 days to fix this problem! – Danield Apr 9 '14 at 8:14
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Google does update crawl errors. The problem is that you need to indicate to them that they're fixed, and they only allow you to mark 1000 as fixed at a time (daily I believe).

Search engine's do not view your sitemap as a definitive list of URLs that exist. It's simply a suggestion for them to start crawling your website. So if you submit a bunch of non-existent URLs, and then change your sitemap to fix them, Google will still have the original URLs in it's index, plus the proper new ones you submitted. That is, until you mark the URLs as "fixed" in Google Webmaster Tools.

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