How to prevent 'drush up' from deleting non native inodes in a sub-theme folder? I installed the theme Basic, did drush up, updated this theme, and BAM, the sub-theme folder I created was deleted.

Gladly, I restored most of it, but why would drush actually delete any non-native folder when it's updating my theme?

Is there something to do to prevent drush from deleting non native inodes in a 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.