I just updated my site to WP 3.6 and Upscale 1.5. After doing that, all my custom sidebar and footer widgets are gone. The ones remaining are the default ones.
I had a pretty customized set of widgets on both sidebars and footer, so it will take me a while to set it back to my customized setup.
The widgets are saved in the database and wp probably deleted the widget/sidebar data. You can try to restore the database if you’ve made a backup (sql file) of the database in the past. You can use tools like phpmyadmin to import the sql file. If you didn’t make a backup there’s basically no chance to recover the widgets. I’d recommend to install a plugin like: http://wordpress.org/plugins/backupwordpress/ to avoid this problem in the future.
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