🚀 go-pugleaf

% [ Warning: The following Names in Name Tree Dests were not defined ] % 
       G10.1116413 
       G10.1116444 
       [etc.] 

These indicate that the automatic hyperlinks for some TOC or Index entries point to missing paragraphs. In my experience, they are caused by editing the document after generating these files. For example, moving a paragraph via cut-and-paste changes its ID number, which is the six-digit number in the named destination, thus breaking TOC links to that paragraph or index entries created from any markers in it. These definitely indicate "dead links" in your TOC or index. To avoid them, always regenerate the book immediately before distilling it. 

% [ Warning: The following Names in Name Tree Dests were defined more than once ] % 
       M79.8.newlink.A 
       M79.8.newlink.B 
       [etc.] 

These indicate duplicate hypertext markers, which are not dead links so much as ambiguous ones. In effect, you have set up links that say go to location A, and then defined multiple location A's. The link will take you to one of them, but it might not be the one you intended. To find these duplicate destinations, search for the marker text "newlink A", "newlink B", and so on (spaces in a hypertext marker are converted to periods in the resulting named destination). The number after the M is the book component number, so the two examples you gave indicate the 79th component of your master book has duplicate hypertext newlink markers.