In Notes 6, you can delete doclinks using NotesRichTextDoclink.Remove. It's much easier to do this if you're working in the back end with a document that's not actually open onscreen at the time. There are examples of advanced Rich Text manipulation in the Rich Text chapter of redbook Domino Designer 6: A Developer's Handbook, including working with doclinks and a discussion of your options when working in documents that are open onscreen.
For earlier Notes versions, you would have to use the Notes C API or third-party tools (e.g., Midas rich text LSX from Geniisoft.com).
This was first published in July 2003