Both wp-includes and wp-admin folders contain core files of WordPress. You should never modify any of them, because it is crucial for WP to be able to change these folders during updates.
Almost the same is true for all WP files placed in root folder – wp-config.php is the only file that WP won’t overwrite for sure.
All your custom code should be placed in wp-content folder. But… To be more precise – the theme files should go into wp-content/themes and they should only define how the site looks, and all other functions should be coded as plugins and placed in wp-content/plugins.
And yes – if you modify any of core directories/files, then you’ll face this problem of overwriting after every update of WP.