I really appreciate the addition in DT3 of the star/asterisk icon (*) to indicate when a file has an annotation linked to it.
However, it seems that the icon remains even after a linked annotation has been deleted—after emptying the trash, executing a ‘verify and repair,’ and restarting, these traces of deleted annotations stick around, and I can’t find a way of getting them to disappear.
Is this perhaps a bug, or am I missing something? Thank you in any case!
I think you need to use the inspector sidebar to choose “Remove” to remove the annotation and the icon 
because this action removes both the annotation file and some hidden link. If you just delete the annotation file in the “Annotations” group, I think the hidden link still remains in the original file.
After some fiddling around, it seems that the problem only occurs with annotations created by the “Annotation Template” script as described here: DEVONthink 3: Annotation Template Missing
Since I prefer to the old way of annotating, as it was done in DT2, wherein the annotation file is created and kept in the same folder as the primary file, perhaps this sticky * icon hiccup is just a minor something I’ll have to deal with occasionally. Not a huge issue, I realize. 
I am/like using the old way in DT 2.n, too because a customised template can be used. You can still getting rid of the icon easily by making sure that the URL field of your pdf file in the inspector bar is emptied after you delete the annotation. 
There it goes. Thank you!