A core upgrade copies all the new files from the distribution over the old ones, so if you changed existing files in the WordPress Default Theme (e.g. wp-content/themes/default/style.css), those changes got overwritten with the new version of that file.
Please note, a core upgrade goes through a list of "old files", as defined in wp-admin/includes/update-core.php, and deletes those files. Any files not on the list, and not in the distribution, are preserved.
Remember, that before upgrades, whether automatic or manual, both the WordPress Files and database should be backed-up as explained in WordPress Backups.
This does mean that you should not modify the default theme, but your changes will not be lost if you create a child theme in a new folder importing the default theme, there are many good tutorials, start by reading the Codex.
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