Strata Site AuditA scan is slow
The crawl requests your own site, and every page it checks is built by WordPress (a page cache rarely helps, since the crawl visits each page once). Images, PDFs, scripts and other files are checked with a quick HEAD request instead of being downloaded. On Pro the crawl starts with two pages at a time, adds more while your site keeps up and backs off when it slows down, so you rarely need to tune it.
On managed hosting (WP Engine, Kinsta, Cloudways and the like) you can also set Pause between requests to 0 and Time per background step to 40 in Settings. A scan started from the Strata screen moves a little faster while that screen stays open. Large Elementor sites take longest in the code stage, which parses every document; that is normal on the first scan.
The link check says it was skipped
Strata checks links by requesting your own pages from the server. Sites behind a password (common on staging) or behind a firewall that blocks the server from calling itself skip this step, and "Sources read" on the Overview says so. Everything else still runs. Remove the password for the scan, or allow requests from the server's own address, and scan Links again.
Pro features are gone after a re-upload
Open Strata, then Account, and click Activate or Reactivate License. Your key is still valid; the re-upload only interrupted the activation.
Scheduled scans do not run
Scheduled scans use WordPress's background job system. If your host disables WP-Cron, it should run a real cron that calls wp-cron.php; check with the host that it does. A scan that has gone quiet is re-queued by Strata's watchdog whenever anyone requests the site, so a site with no visitors overnight may simply be waiting for the first request of the morning. You can also run wp strata scan from a real cron; see WP-CLI.
A scan stopped with "stalled"
Strata stops a scan that makes no progress for two steps in a row and says why. The usual causes are a PHP time limit shorter than the background step (lower Time per background step in Settings) or a host that pauses background requests. Start the scan again; it does not need to repeat finished stages. If the host kills a step part way, the watchdog clears it and starts a fresh one within about five minutes, and Resume does the same at once. When nothing has moved for a while the header says it is waiting for the host to run the next step and offers Resume.
A file is marked "likely unused" but I use it
Strata checks post and page content (including drafts), featured images, WooCommerce galleries, Elementor data, the site icon and logo, and custom CSS. A file can still be used from places it cannot see: theme options of some themes, hard-coded paths in PHP, widgets, custom fields, emails or other websites. Strata checks again just before it moves a file to the trash, but look over a file before you remove it. Ignore the issue and it drops out of the score.
What leaves the site
Scans run entirely on your server. Strata contacts outside servers only in these cases, and only when you choose them: the optional parent theme comparison downloads the matching theme release from WordPress.org; Freemius handles licensing and the optional usage opt-in for Pro; Slack alerts (Pro) send the alert text to the webhook you add; external link checks (Pro) request the external addresses linked from your content. See the privacy page.
What happens when I delete the plugin
Deleting Strata from the Plugins screen removes its database tables, settings and scheduled jobs on every site. Changes you made with Strata's fixes stay as they are. Deactivating keeps everything.