Hi there,
For these purposes, Penscratch 2 is an entirely different theme, not just an update to an already-installed theme.
Penscratch 2 still has the sidebar widget area, so your widgets should be unaffected, as will your menu. However, it looks like the custom header image might not stick, nor will any additional CSS you added in the Customizer.
But if you download the .zip for Penscratch 2 and install it via WP-Admin, you can use the Live Preview feature to open the new theme in the Customizer without activating it. Then you can add your necessary customizations there before activating the theme. Just open the Customizer for your current live site in a separate browser tab, and you should be able to copy your customizations from the one to the other.
In this case, don’t install the theme via the Jetpack interface on WordPress.com, as that will install and immediately activate the new theme.
Here’s a tutorial on the process if you’re not sure what I’m referring to.