Personally, and bearing in mind I'm not a physiotherapist, just some person on the internet with an interest for biomechanics, I would opt for stretching both calves and hamstrings throughout the day. Muscles do shorten with disuse or more accurately with overuse of certain positions rather than others (sitting, for example). But they can lengthen again if you keep putting them in positions where they need to be long.
I really recommend having a read of the blog posts/articles over at katysays.com - I'm not affiliated in any way but I find the site to be very informative and easy to understand. There are lots of stretches and exercises put forward for calves, hamstrings and generally correcting various issues with pain and mobility. Also very encouraging about these things being changeable if you give your body the right circumstances!