Sorry I expected "the usual suspects" to have jumped in by now but perhaps they are having time off or asleep
In direct answer to your question, it depends on what merge setting you have set in Calibre, under Preferences->Adding books.
If you have ticked the "If books with similar titles and authors found, merge the new files automatically" box, then any book formats which are the same as those that exist in Calibre will be ignored. So you can "safely" re-add the entire directory.
If you don't have that ticked, then my understanding is that Calibre will detect duplicates based on book title, and prompt you asking if you want to merge or create a new book for each. That could get pretty painful for a large directory.
If you are still concerned about which option to choose, just move all the stuff you have added recently into a different folder and add from there. If you use windows and right-click on the columns in windows explorer there is bound to be one of the date columns which will reflect the date you put the file in the folder if you can't rely on other dates the files may have.