Hi Rene,
These files should not be deleted, even if it seems that they are duplicates. They are being created by MSHelp runtime during installation of the products that install hxs files and register hxs namespaces (for example, MSDN libraries, MSDN Express, VS Express skus, Visual Studio, .NET SDK, and many other SDKs)
If you delete any of the files, it might cause some or all documentation to stop working. It will be really hard/impossible to recover from this situation.
Some of the files are created on a first use of the documentation. They contain merged index and other information to have MSHelp-based product function correctly. Please treat them similar to registry.
Please let me know if you have any further questions,
Maria Shneerson, MSDN