Errors displayed during core upgrade
Just move your entire Drupal root somewhere else, and put something else in its place (with a "Be Right Back"-message) while the upgrade goes on.

For instance, if your Drupal root is /var/www/html, prepare a directory named /var/www/brb and put a static index.html-file in it with your BRB message.

Then execute the following pair of commands:

mv /var/www/html /var/www/pending_upgrade
mv /var/www/brb /var/www/html


Now, make sure that your ftp job puts the files in below /var/www/pending_upgrade.

When done, restore your site with the following pair of commands:

mv /var/www/html /var/www/brb
mv /var/www/pending_upgrade /var/www/html 


The above assumes that you have CLI access.  If you don't, most ftp tools have built-in commands to move directories around.