This happened most recently with 6.10 to 6.11, but it seems to happen when I add modules as well. I have a template which uses some included javascript files in 'js' folder off the root. It's a template I inherited from another consulting company, which doesn't mean anything other than the goal was to build a new site using this template, which I had to migrate from 5 to 6, and it worked fine for a few months.
Seems shortly after the 6.9 to 6.10 upgrade, every time I'd add a new module, or need to run update.php, it would go out and delete all the files in my 'js' folder. Happened again today when I did the 6.10 to 6.11 upgrade. Originally I thought the issue was related to installing a module to help with Active Directory, but after rolling back to a version I had before I installed that module, I'm realizing it has nothing to do with that modules. In fact, I watched it delete the files while doing the update.php step 'before' re-enabling all my non-core modules. When I upgraded a second application, I marked those files read-only, and while it doesn't delete them now, I get lots of logged 'unlink' errors, saying the permission was denied (which is fine with me).
warning: unlink(js/one_of_my_files.js) [function.unlink]: Permission denied in D:\xampp\htdocs\intranet\includes\file.inc on line 435.