Could you provide more information? Is the other file completely different? Or is it just an updated version of the original? If the latter, then you can open the original and use Replace Pages (under Document menu, then Pages) and you're bookmarks will remain linking to the same places. You might have to reset some of the destinations if the piece of text has moved, for example, but it could still save you a lot of time.
Alternatively, if the former, you could get the new file and then do an Insert Pages (again, under Document menu, then Pages), inserting the original. This will copy over the bookmarks as well. You could then delete the new pages (again, under Document menu, then Pages) and have the bookmarks remain. You would still need to go through them all setting the destinations, but if you keyed in the Bookmarks in the first place, this might save some time.
If neither of these options is relevant, could you post some more information?