If I update WordPress my custom data will be deleted from the wp_users table?

It is possible, especially if the update includes changes to the user table. The only way to be sure is to test it, but for future reference:

Never modify the scheme of WordPress Tables

If you need to add additional information about something, WordPress provides meta, user meta, site meta, post meta, comment meta. You may know these as custom fields.

For example:

$value = get_user_meta( $user_id, 'example', true );
update_user_meta( $user_id, 'example', 'newvalue' );
$all_meta = get_user_meta( $user_id );

Adding columns manually to tables also bypasses the caching layer slowing things down, encourages writing manual SQL statements ( you could have used the WP_User_Query class! ), and stops the information being imported/exported ( custom post types get put in content exports, custom tables don’t )

I recommend writing a small WP CLI command to fetch each user and store these columns as user meta instead