Add the annotated version to the existing book as <whatever>.ANNOT-PDF and tell your OS to open .ANNOT_PDFs with your PDF Viewer.
Or, keep the original and annotated versions in a separate libraries and use the
The calibre:// URL scheme to link the books in the
Originals library to the same book in the
Annotated library (and perhaps vice versa).
I use the latter because I sometimes have multiple versions - annotated, translated, illustrated.
The
calibre:// URL Scheme is a recently added enhancement.
BR