[Plugin: Admin Menu Editor] Export Menu Configuration

Possible explanation:

If the menu configuration contains any URLs that refer to the old site URL, and you used search & replace to update the URLs in all wp_options entries to the production URL, it may have corrupted the plugin configuration.

This is because the configuration is stored as a serialized PHP array. When PHP serializes a string (e.g. an URL), it stores not just the string itself, but also it’s length. Modifying the string without updating the stored length will make the serialized value invalid.

Upgrading to Pro could help because it includes a menu export/import feature. You could export the configuration, copy the DB, then import the previous configuration.