If your Audyssey settings survived the update, then so did the calibration data. I can't explain why you noticed this change in volume, unless you have DynVol on now but didn't before. I had no disruption of my x4000 after the update.
AT&T U-Verse Northeast Ohio
Denon x4000, Carver m1.0t, Samsung LED TV, B&W 704 mains, two M&K subwoofers, Oppo 103, Roku 2, etc.
Headphone system: Sennheiser HD600, AKG K702, Hifiman HE-400i, Marantz HD-DAC1 (also used for music playback in the main system, Marantz CD5004, Denon DVD-3910