If with "last update", you mean the hotfix that has been released yesterday, I can't see how it could possibly affect navdata, since it doesn't download anything related to that, just a fix for the main program to fix crashes with some 3rd party airplanes.
If with "last update", instead, you mean the one *before* that, it has updated the Navdata, but it hasn't affected KORD.
In any case, I cannot reproduce the problem, see the attached screenshot, which shows RWY 28C working normally, including STAR and Approach, and you can see the simulator is the very latest version released yesterday.
You mentioned Navigraph so, the real problem here is that, for some reason, updating the Navdata using Navigraph has caused a problem that doesn't happen normally.
MAYBE it's related to the fact latest AIRAC added the new RWY 9C, which is not there in the scenery ( yet, we are working on it right now ), but it's difficult to say why this affected other runways without looking at the data from Navigraph.
We found a strange glitch in the sim that, if a runway doesn't include its Start position, it disappears from the map, and THIS happened after a recent update, so perhaps if Navigraph is removing the start positions without redefining them, they are making the runways disappear, but only at 3rd party airports that redefined the runway and their starts on their own.