BuddyPress.org

Child themes do not get deleted, only the files inside wp-content/plugins/buddpress/bp-theme

This is why you never modify those files. if you want to change those files, then you copy them to your child theme folder preserving the folder structure.

If you want to change the header then you copy over the header.php to child them folder and BP will use this file instead of the one in the plugins folder. No fear of it getting wiped out on upgrades.