After what feels like creating a million new PDFs, it's important to double check your notes from each collection you viewed in the archive. Make sure you have a file or photocopy for each document that you recorded photographing or copying in your notes. It's better to realize that something is missing right after your research trip, because with fresh memory you might recall if your notes are in error. If this does not seem to be the case, I recommend checking the documents before and after the missing one--sometimes photos seem to be part of the same set rather than two separate items and so you accidentally stick them together in one PDF.
Re-reading archival notes right after a research trip is akin to having to edit a paper immediately after writing it. It's utter torture and requires superhuman willpower to slowly move your eyes from line to line. It is, however, the best way to get an A (at least for effort).