How to prevent 'drush up' from deleting non native inodes in a sub-theme folder?
If your sub-theme folder is inside the base theme folder, it will get wiped out when there is an update to the base theme, as drush will remove the contents of the theme folder and replace them with the new updated contents of the theme.

The solution is to move the sub-theme folder to be along-side the base theme folder, so it's a sibling, rather than a child.