WordPress replaces the supplied Themes on each upgrade. On this forum, I have seen the recommendation that, if you use one of the supplied Themes, rather than a Theme you have installed from the Themes Directory, that you copy it (the supplied theme folder) to another theme folder that you create yourself.
That's OK, but you really should be checking to see if there have been any meaningful changes to the Theme files after each upgrade. Otherwise, you will be running with an old version that may have security holes, incompatibilities, etc. Admittedly, a rather small risk.
But, with that in mind, I don't create a new Theme folder. I let WordPress replace the contents during an Upgrade. I go through a process for each upgrade that sees me compare each theme file between a Vanilla (unmodified by me) copy of the old and new versions of WordPress. If there are any changes to any of the theme files that I have changed, then I make those changes to my old version's modified theme file (or vice versa, making my changes to the new version supplied by WordPress).
Then I simply let WordPress do its upgrade and immediately replace the upgraded theme files with only those that I changed in the previous version, after making any changes noted in the last paragraph.
Because this problem goes beyond just Theme files, I keep a Change Control folder on my own machine that contains only the Wordpress files that I have changed, in the same folder structure as on the web server. This allows me to easily find and, more important, FTP upgrade these changes to multiple WordPress sites quickly, right after each upgrade.