Certainly the retired (but can be reinstated) “Insert cross references or notes” script allows you to choose a particular book or books to insert references into.
But my guess is that if you used the new “Insert cross-references” function (which is said to be going to work in the PT 9.1 upgrade) then you could check the delete all existing cross-references option to obviate continual doubling up of the references every time you ran the script.
Maybe someone knows why that wouldn’t work or shouldn’t be done?
EpiWaetMan