Error message when deleting folders/files on Maintenance mode
Rather than the two step deleting the folders and then uploading the new ones, I would recommend just copying over the old ones with new ones. You'll probably have to tell your FTP program to overwrite but when I upgrade in this fashion, I select all the files and directories except for sites folder and push them to the server.

When possible, I use the Drush tool via a terminal window as it is a much quicker and easier solution.