Just make sure you're checking your books periodically through the run. The main downside to this method is that if the printer double-feeds or jams then every book after that can end up in the wrong order. When doing a longer run I usually walk over to the machine and randomly check a book periodically - check the middle of the books to make sure the middle page is still the right one. If the machine jams for any reason make sure you cancel the job, and reset the stack to a full set before restarting it.