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My eCommerce store is 2 years old. Previously, I have not promoted it and the links were not built for SEO.

In connection with the change of CMS, 90% of the pages link structure changed and because of that they got beaten and a lot of garbage appeared in the Google index. I decided to completely clean up the index and deleted all the non-required pages through the Google Webmasters' panel, and then again added the correct links for the second index.

But for some reason, even after 3 days, Google did not index the pages of my store. Can someone tell me what is exactly happening? And how long can Google take to get the store indexed?

Did you get any notification that the pages will not get indexed?

You did all that was not right for your website. Now you will need to wait because it is a long and tedious process. Check the 404 errors issue in the webmaster tool and try to fix that.

You did all that was not right for your website. Now you will need to wait because it is a long and tedious process. Check the 404 errors issue in the webmaster tool and try to fix that.

I cleaned all the issue, including from the BIT pages that gave the code 404.

As I wrote above, after the change of CMS in the search, there were about 3500 broken pages and only 200 live.

Is it not easier to remove everything from the index and re-index the site as it was already which had 2000 pages without broken links?

Google will consider them as new pages, and not old (you changed URLs) - will be non-unique content, since old pages, in its algorithms are still alive. 301 should have been updated! Positions can persist strongly, 2 days are not deadline, add redirect to new pages now.

1) About the content, I did not understand because I checked a bunch of services - my content is indexed, it is unique because my site is not present in the index. Is there any algorithm for this?

2) Already had a good amount of organic traffic per month, but did not observe the pages of the store.

It may be simpler, as Amrit wrote, such "simple" changes will entail the problems described above. Besides this, the weight of the old pages will not be transmitted either. And position as well.

What weight are we talking about, if for 15 days 5 visitors from organic search matter?

Kapil, it was necessary to do redirects. Now you will need to wait really long. Periodically update and submit the sitemap in webmaster tools for re-passing, the best option is to add most important pages manually at the same time. Hope this helps.

When you launch any website, your first approach is to see everyone your website on Google. Actually, Google first checks the website, that time period, also called as Google sandbox time. Google may take between 4 days to many weeks depending on the type of the website or content on this website. Google has many algorithms for crawling or indexing the contents or websites. Many factors are considered for indexing in Google like sitemap's, hyperlinks, quality contents, and much more.
Google crawls any website, through crawlers or known as Googlebot. When crawler's come on any website they first check website's sitemap, if they found all website's links in sitemap then they index or save all links in their database or server. So, the sitemap is very important as an indexing point of view. Also can submit website to the high authority social bookmarking sites for faster crawling, because this bookmarking sites can crawl through Googlebot by Google periodically.