Sounds like you deleted some terms and/or taxonomies related to menus. You need to get those back into the database.
Easiest solution is if you took a database backup before removing those terms, as is best practice, just restore your database. Or if the host provides automated backups, use one of those.
If you don’t have any database backup, this gets a bit off-topic into more specific theme setup, but generally speaking you should switch to a default theme (i.e. Twenty Seventeen) and then try switching back to your desired theme. If that doesn’t resolve the issue, you may need to start from scratch on a new WP install, export the content from the old site, import it into the new site, and manually configure all the theme settings. It’s possible that if you have a fresh WP install and you copy its wp_term_taxonomy table into your current install, that may help.
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