Well, as already said by Archangel, there were newer, updated War Sphinxes which were built alongside the Builder Security's "Seekers". This could possibly be one (or maybe two conjoined) new Sphinxes.
"It would also make sense that there is a War Sphinx on or near the Ark (Forerunners kinda guarded that thing religiously, and my bet is that Bornstellar sealed himself in a Cryptum there, which would be mighty interesting."
Other than Bornstellar going into isolation via a cryptum, this makes sense. I could definitely see a Halo 5 trailer depicting the heightened sense of security around the isoDidact, since Ur-Didact absolutely detests him.
Actually, I guess before I make assumptions (and since I didn't read Silentium), how far in the past was Silentium dated compared to the events in Halo 4?