I would not recommend to change data such as usernames directly in the database, since you might break something….
Having said that I presume you have forgotten to add your new admin username to the site_admins option in your wp_sitemeta database table, therefor you won’t see the Network Menu, because your new username is not a site (network) admin.
NB: Keep in mind the site_admins option is a serialized array!
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