From the INSTALLATION section of the Readme.
AUTO INSTALLER!! No more external SQL files needed to install/upgrade Edit Orders.. Yep that's right.. The Edit Orders install/upgrade is easier than ever!!! Whether you are upgrading from a previous Super Orders install or doing a vanilla Edit Orders install, the newauto installer has got you covered. Please note: Uninstall is not automated. So to uninstall you will still need to use an external SQL file.
followed shortly by
DO NOT RUN OLDER VERSIONS OF THE INSTALL/UPGRADE SQL FILES when installing/upgrading!!!!!! Doing so will cause issues with your Edit Orders v4.0 install.
In upgrading to Edit Orders 4.1 from Edit Orders 4.04, and with SuperOrders 4.0.5 already installed, I understand that the two (2) orders.php in 2_Modified_Core_Files are not to be uploaded.
Also that admin\includes\functions\extra_functions\common_orders_functions.php is identical to that in EO 4.04, both essentially blank files and deprecated, so it makes no real difference whether the EO 4.1 version of this file is uploaded or not.
However, it is not clear from the instructions whether the EO 4.04 edit_orders_uninstall.sql file needs to be run, and all or any EO 4.04 files need to be removed, prior to uploading the EO 4.1 fileset.
Clarity appreciated.
ps if EO 4.1 is about to revised, the Readme could do with less hype and clearer instructions.