I don’t think it’s a good approach. Themes shouldn’t change any settings and definitely not settings like permalink structure.
If I’ve set my permalinks structure to given one, then I had my reasons to do it. Such change have many effects. If you change the permalink structure you cause many SEO problems. But also – the site may stop working at all (for example if the server doesn’t support permalinks at all or if it doesn’t have access rights to .htaccess file).
So… The real question is not how to force WP to recalculate the permalinks, but who to avoid such operation at all.
If you really need a permalink structure to be set to given one, then you can politely ask user to change it using admin notice.
But to be honest, I really doubt that a theme should require such changes. It should work with any permalink structure.