I hope this reply is in the right place - it is for Laura.
I have a large FTM media folder with JPG files of all pages I cite in all censuses, parish records, electoral roles etc - nearly 4,000 JPGs.
RM import correctly points to each JPG - which impressed me.
I have edited each JPG to include the "FTM Person number" of all relevant people. So a single JPG Census return page will have all members of one, or more, families listed and along side them their Person ID/Record Identification Number. Generally 1-10 numbers added to each JPG.
This is not a paper file which has been annotated but the demand is similar.
Changing all the annotated JPGs would not only be a very long task it would be difficult to ensure accuracy as the numbers are integrated into the image and not searchable.