No deletion of theme folders for any BP upgrade. Have you checked if the theme folders have indeed been deleted in wp-content/themes/ via FTP/FileManager/etc?
It doesn’t, it simply disables them and moves to the incomplete folder inside the wp interface. It requires bp-default to move on, I have the same problem but no one seems to know or to care. https://buddypress.org/support/topic/bp-default-required-after-wp-3-5-bp-1-6-2/
It DOES delete the theme folders. I was in the directory via ftp, hit the update, refreshed ftp, and they were gone. This happened on 3 sites. I could not access the front end of my sites, as there was now no theme associated with it.
It really doesn’t. I assume we’re talking about WP’s /themes/ folder. If you’ve been sticking themes inside /plugins/buddypress/BuddyPress-themes/, then yes, they would be removed (don’t store custom themes there).
BP does not delete files outside it’s own directory, no plugin would any files or directories in /wp-content/themes/ would never be touched.