🧭 Overview
When you rebuild your website, switch themes, or migrate to a new platform (such as moving to a new Shopify theme), Search Atlas may continue surfacing SEO issues tied to your old site structure. This happens because your project is still linked to the previous website configuration. This article explains how to reset your project data so it accurately reflects your new site.
⚠️ Why Old SEO Issues Keep Appearing
Search Atlas stores a snapshot of your website's structure, pages, and technical SEO data when a project is first crawled and connected. After a major rebuild or theme migration, this stored data becomes outdated. Common symptoms include:
- SEO issues flagged for pages that no longer exist
- Missing recommendations for new pages added during the rebuild
- OTTO continuing to reference your old WordPress setup after migrating away
- Audit scores that do not reflect your current site
🛠️ Step 1 — Disconnect Your Old Site Connection
If your project was previously connected to a WordPress site and you have since migrated away, the WordPress link must be cleared before new data can be pulled correctly.
- Log in to your Search Atlas account.
- Navigate to the project affected by the migration.
- Open OTTO SEO for that project.
- Go to the project settings and look for the connected site or WordPress integration.
- Select the option to disconnect or unlink the existing site connection.
If you do not see a disconnect option, or if your project is one of the cases where the WordPress link is stuck, contact support using the chat widget (see the end of this article). Our team can manually unlink the old connection on your behalf.
🔍 Step 2 — Re-Crawl Your Website
Once the old connection is cleared, trigger a fresh crawl so Search Atlas can index your rebuilt site from scratch.
- From the left sidebar, go to Website Studio (or navigate to /website-studio).
- Select your project from the project list.
- Locate the Crawl or Re-crawl Site option within the project settings.
- Confirm the crawl. Depending on your site size, this may take a few minutes to complete.
Once the crawl finishes, Search Atlas will display SEO data based on your current site structure, not your previous theme or build.
📊 Step 3 — Review and Re-Activate OTTO
After the re-crawl is complete, review your OTTO SEO recommendations to ensure they reflect your new site.
- Open OTTO SEO for the project.
- Check that the connected domain matches your live, rebuilt website.
- Review the updated list of SEO tasks and deploy fixes that apply to your new theme or structure.
- Dismiss or archive any tasks that were carried over from the old site if they no longer apply.
Note: If OTTO is still showing tasks from your old site after the re-crawl, try deactivating and reactivating OTTO on the project to force a full refresh of its task list.
💡 Tips for a Smooth Reset
- Do this after your new theme or site is fully live — crawling a site that is still mid-migration may produce inaccurate results.
- Check your sitemap — make sure your new site has an updated sitemap submitted so the crawler picks up all new pages.
- Allow up to 24 hours for all metrics and scores to fully update across your dashboard after a re-crawl.
- Shopify users: If you switched to a new Shopify theme that significantly changed your URL structure, treat this as a full site migration and follow all steps above from the beginning.
🙋 Need More Help?
If you need further assistance, open the chat widget in the bottom-right corner of the platform and type human teammate to be connected with a member of our team.