This issue is resolved in Dimensions 10.1.3.  This applies to Dimensions CM 10.1, 10.1.1 or 10.1.2 customers who are performing removal of folders in projects that have attached deployment areas that contain files not under Dimensions control.
 
In Dimensions CM 10.1 or 10.1.1 when a folder is deleted from a Dimensions project that folder is also deleted in all deployment areas associated with the project.  If the folder on disk in the deployment area contains files that were not placed there using Dimensions CM deployment functionality those files will also be removed.  A folder can only be removed from a Dimensions CM project when it is empty (when all the items in that folder have been removed) but customers should consider that despite the folder in the Dimensions project being empty, the corresponding folder on disk in deployment areas might not be empty.
 
In Dimensions CM 10.1.2 when a folder is deleted from a Dimensions project that folder is only removed from areas associated with the first stage.  Other deployment areas are only affected when the AUDIT feature is used on the area.  When AUDIT removes folders from a deployment area the same issue described in the 10.1.1 section above can occur.  If there are other files that were not under Dimensions control in that folder they will be removed, regardless of file permissions.

Logged as DEF137862

If  using Dimensions deployment in such a fashion that this issue may affect you, as an immediate wokaround use current projects for development and testing deployment only.  Create separate projects for production deployment to eliminate the potential impact on production environments.