Upgrade unsets widgets

Hi,

I recently tested an update from 3.6.7 to the most recent version of Atahualpa on a number of WP sites I have it, and there were issues. The administrative toolbar was not missing, and the widgets were unset.

I've looked through past forums, and it seems like this is a known problem, and the workaround is to manually re-place the widgets. I'm hoping to avoid that, as I have ~60 affected sites.

Is this still the recommended workaround, or are there any other recommendations available? Might it work if we do a clean install of WordPress on a separate server with an up-to-date theme and then migrate the database to that installation?

Thanks for any help you can provide