I have several WordPress installs handling offline tasks for other sites and they all have that same ‘discourage’ setting. That’s just a suggestion to search engines not to index but they can still spider the site if they want to.
If you haven’t done so already then install the Health Check plugin and run that to see what it might report.
https://www.ads-software.com/plugins/health-check/
If you think it could possibly be related to the new Block Editor and a mismatch with your present theme then you might install and activate the Classic Editor plugin to revert your editor back to the Tiny MCE editor.
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