you still must not be doing the proper update method.
you are supposed to be downloading the complete zip package. not the auto update package.
when you are following the instructions I linked to above, there is no modifed files to work with at all.
you just upload all new files except for the config.php file and then go to the install folder in your browser.
you then click on update, you then click on update database you then click on update database only.
at no time will you see anything about downloading files or uploading files or modified files etc.
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