For several years, we have used a local QNAP-enabled hard drive array to sync with Box. That way, we always have a local copy of all files under our direct control.
We recently upgraded to a new HD array and had to re-sync with Box. Box has now created thousands of duplicated files both on the HD array and on Box. It's a horrible mess. It has to be a Box issue because the HD array is just that, just a hard drive. And we can tell it is Box because of the file name extensions being added to the duplicated files.