Yes, the games at Olympia continued right through the war, and were often used as a convenient place for conference.

In Book III, Thucydides tells us that representatives from Mytilene were instructed to meet the Spartan envoys at Olympia during the games to talk business (3.8ff). The Mytilineans, during their speech, even invoke Zeus the Olympian. They then conclude an alliance, and the Spartans go on to discuss their war plans for the coming months (presumably still at Olympia).

In Book V, Thucydides tells us a confusing anecdote in which the Eleans (who controlled the territory around Olympia) barred the Spartans from the games as punishment for Spartan military activity in their territory, apparently in violation of the universally-understood truce which held in all territories in which there were PanHellenic games happening (Olympia, Delphi, Isthmia, and Nemea). It is a confusing situation, since the Spartans claim they weren't notified of the truce (but it was supposed to be on by default during the games?). You can read what Thuc has to say beginning in chapter 49 of book V. This is the most discussion we get of the matter of military truces during the games.