Tonight I had cause to modify an annotation file from inside Logos. 

The story was that I'd given a friend one of my annotation (note) files and he'd then updated it and given it back to me with his annotations in it.  When I opened Logos with the annotation file in the right location (<My Documents>\Libronix LDS\Annotations) Logos knew nothing about the file - it was the same name as one I already had there and the one I had was more recent so Logos didn't recognize it.

So I opened the annotation file using EditPlus (a favourite text editor of mine from the old days) and found (happily) that the file is simply XML with a custom schema.

It turns out that each annotation is encapsulated by <annotation></annotation> tags.  So - to drop an annotation into an existing file all you need to do is copy the tags and everything in between them at the end of the existing annotation file just before the </lbx-annotations> tag.

Simple.

Typically you wont need to do this, but in case you do  - now you know how to do it.