Question: Document with attachments is opened in XPage. I want to edit attachment in associated program (say MS Word or Excel) and save changes back to Notes document.

I am aware of webdav configuration, but it have significant caveats: attachments are no longer stored within related document and security is controlled by ACL and not RN/AN.

How to edit document attachments in web client? Did any of you implemented such feature?

Answer: 
WebDAV is the way to go. There's an implementation that can read/write DominonAttachments. Soon on OpenNTF
The tool we use, with recent improvements for XPages, is Swing: <http://www.swingsoftware.com/>

We checked many others, without success.