You can run APM in so called 'incremental' mode. That means, after the first APM session, simply run APM again. If there are unlinked articles and empty or incomplete pages, APM will process those, leaving alone the complete pages and linked articles.

Be aware, however, that the Repeating Shapes check won't work in the incremental mode, and therefore, you may end up with the two consecutive pages paginated with the same shape. That is because the repeating shapes check works only in the session, and only for the newly paginated pages. Therefore, instead to run APM in the incremental mode, we recommend you to unpaginate all and then to repaginate.