I know we've been talking about this since the Beta so the conversation is nothing new, but a proposed solution came to me that I thought makes a lot of sense.
Problem: When I make a highlighting its not all that easy to find out where the note for that highlighting is. Even if I keep things organized in the future it could become difficult to navigate to a note attached to a highlighting.
Solution: Right click on an annotated section and "annotations" will be a selection in the right column. select it and there will be sections on the left for each layer of highlighting present. Each section would have the following options (or some of them):
Remove This layer (Keep Note)
Remove This Layer (Remove note)
Edit note
Above the first section could be an option to remove all layers.