For the live site, you can safely fun EO's uninstall_eo.sql commands (see below) ... without removing any files. After removing the configuration-related elements from the database, just refresh the page and the current database-based configuration elements will be re-applied.
Code:
DELETE FROM configuration WHERE configuration_key LIKE 'EO_%';
DELETE FROM configuration_group WHERE configuration_group_title = 'Edit Orders' LIMIT 1;
DELETE FROM admin_pages WHERE page_key IN ('editOrders', 'configEditOrders');
Also noting that the "Shipping Tax" setting was removed in EO 4.1.1.
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