When upgrading the theme, I had to go into the functions and remove the lines that looked like:
'id'=> __('left-sidebar', TEMPLATE_DOMAIN), in the widget area registration sections, or the old widget areas became orphaned. turning into "inactive widget areas".
I tried just changing the id to match the old names (caps on L and S) but that didn't work. Interestingly enough the widget areas seem to work with the description still there, but the name's didn't even have to be identical (could remove - from 'name') to the old and they worked.