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Let me start by thanking you for the amazing work you've done with AT3.x, it's phenomenal and makes doing responsive sites so easy / clean.
At my agency, we have a local / DEV / TST / PRD deployment workflow. When we commit to our VCS from our local boxes, it auto builds to our DEV environment for collaborative testing. During the build, we exclude any files under public:// to keep the build time down. Since AdaptiveTheme stores it's theme built css/info under public://adaptivetheme, those files never make it onto the DEV server. AdaptiveTheme doesn't do any check to make sure they exist, nor does it currently rebuild them on a site/theme registry cache clear.
It took a while for us to figure out why the site looked different on our DEV box vs our Themer's box and we traced it back to those files being missing. Of course going into the theme settings and re-saving them created the files and fixed the issue, but for others doing this type of dev, they'll likely run into the same confusion.
Since the files are being generated and cached under the public:// directory, it stands to reason that they could/should be rebuilt on a cache clear. When something doesn't look right on the site during development, it's pretty standard practice to just clear the cache to see if it fixes it... so it'd be a quick way to handle this that would be intuitive. If you disagree that's fine - I will defer to your judgement, but I figured I would bring this up and see what you think.