What could make it not work is that you renamed the note in Evernote after having created the link to the note.
Ex : My Note 1 contains a link to My Note 2
[Title = My Note 2]Link
After that, you rename "My Note 2" to "This is my note 2". The link in My Note 1 will be updated, but not the Title of the link. Since the matching is done with the title of the link and the note title, the plugin won't be able to find the note after the import and won't be able to replace.
Clear ? 
Perfectly clear, and it could explain some of my broken links. But not for some, as in the example provided (screenshots) I was asking for help/advice. I didn't rename the note after creating a link referencing it. I created the summary note contaning the internals link at the very end before export, no rename or content update. So I have no clue 
EDIT : if you closely look at my screenshots, despite the long note title for which I'm sorry, the names match exactly...
I think the plugin and the app do things differently. If the app cannot be sure what the target of a link is, it's going to leave the evernote:// link while I think the plugin will change it anyway. It's documented here:
Another issue is that the app currently only processes links within the same notebook. So if you have an Evernote link in Notebook1 that links to a note in Notebook2 it's not going to be processed. This is more a limitation of the app at the moment, and something I'd like to fix