Honestly what I do, is download the wordpress to my desk, delete wp-content folder, and wp-config or wp-config sample from the fresh download folder, then rezip it
I then delete the files off my server, except for wp-content folder and wp-config.php file (which I back up before I start any of this, just in case)
Then I upload my custom zip folder (with the removed file and folder) to my server
I unzip the folder on the server And place the files
HOWEVER- if you now have admin access, you can go to upgrade section and do a 1 click upgrade to the same version to reinstall, which often works for me when I break something