Do you have any other devices (analog or digital) connected to the AVR which would exercise the subwoofer output? If you don't have other sources, you might try connecting the player's analog audio outputs to see if they can cause subwoofer activity. If they don't, then the problem is in the receiver.
I also suggest running MCACC and/or the manual speaker setup again, just to make sure that the receiver's sub output is still working with test tones.
Another worry is that HDMI circuitry in general is extremely fragile. Swapping connections while power is still on has been known to damage it, for example, although I'd expect that to affect video, too, not just the low audio frequencies.
Marantz SR7009/7.1.4/FH+TM/DefTech PM1000/LCR+TM amped