The drawing of the text/comment bubbles is entirely in the PDFViewWPFTools project, so you need to make the following changes, and then make the call yourself to trigger.
1. Add the following method to NoteManager.cs
internal void CloseNotes()
var tempDict = new Dictionary<Markup, NoteHost>(mActiveNotes);
foreach (KeyValuePair<Markup, NoteHost> entry in tempDict)
2. In ToolManager.cs add the following method
public void CloseNotes()
Then in your code, call ToolManager.CloseNotes();