It might be interesting to look at the Appendix to Exposé I of SGA 4. In a footnote this is described as follows:

Nous reproduisons ici, avec son accord, des papiers secrets de N. BOURBAKI.

While the appendix treats mainly the theory of universes, it makes use of the language of categories. Moreover, some internal references hint to the existence of some more "papiers secrets" containing a draft of a chapter about categories.