I’ve finally found a (very obvious; I can’t believe I didn’t think of it before) solution to something that bugging me with LibreOffice Writer.
If you delete a comment in a Writer document when you have tracked changes enabled, the comment remains visible.
Using the “delete comment” function in the comments menu, the comment remains visible.
My previous workaround
Try to remember to turn off tracked changes before deleting comments.
Actual (really obvious) solution
If you delete a comment when tracked changes are enabled, the deletion of the comment is, in itself, a tracked change. In other words, the document (correctly, now that I understand it) shows that the comment existed but has been deleted.
To remove the comment from the document, accept the change.
Easy when you know how!