After converting pdf and Word documents from the Web into books, I systematically convert the archival name fro the Web source into something more suggestive and closer to a bibliographic note
Thus "106491e" becomes "1964 OECD Economic Survey Ireland".
After doing this hundreds pf times and then beginning to work with the notes I had highlighted, I discovered with horror that the notes retained the old unsuggestive archival name, making it much more difficult to work with them systematically.
Being able to sync note names with book names would be very useful, and I am a little surprised that this has been overlooked!
I use MARGINNOTE PRO. For several hours every day to do the background research for a book I am writing.