Nothing in the update can possibly change this.
GSX will read the AFCAD in scenery area priority order and if an AFCAD is not read, there might be many reasons ( not complete, too big, corrupted, not in the correct order, etc.), and none of them have anything to do with the update.
You can try enabling Logging in the Troubleshooting section of the GSX Settings, and choose "Restart and rebuild the airport cache" in the Couatl menu.
After the cache has been rebuilt, exit the sim and check the log file at %APPDATA%\Virtuali\Couatl.LOG, if it says some files has been rejected and why.