[Geoff Bacon]

Annotations are stored in the database rather than in the pdf. This means that if you use MSP interfaces to change the file then you probably lose the annotations.
I believe that locating the file and manually replacing it outside MSP should work (but only if you are not reordering the pages in the file)

Should that not work then, for a small number of songs, I would have left the bulk of the large pdf and song entries unchanged and added new, separate, modified pdfs for the changed songs.

Alternatively, I suspect you could export the main pdf with the annotations embedded, use a pdf application to replace the necessary pages and use MSP to reimport/replace the pdf.
The disadvantage is that you might not be able to edit the embedded annotations and/or the MSP may take longer to process the file when loaded (I can't remember which of these applies)

One of my groups uses a multi song pdf and I have split it into individual pdf's. This is because I don't manage the book and have no control over where songs are inserted in it (requiring major editing of the CSV file, possibly affecting cropping if the page has been reformatted and maintaining the annotations). I suggest you split it into single PDFs together with loading the big pdf as a fall back in the event that you haven't noticed one a changed song).

Others may suggest different approaches

Geoff