So, I found out this neat little sequence using the latest version of Notepad++
- Open the document
- hit Ctrl-F
- In this find window, go to the "Mark" tab
- make sure the "Bookmark" is checked
- place what you are looking for in the "Find what" field
- Mark all
- Now close this and go up to the search menu
- Do a search "Bookmark"
- in here are options to strip out all bookmarks or copy all bookmarks
For my use case I needed to copy all the bookmarks and paste them into a fresh document.