Changing the HDMI cable can't affect only the subwoofer. It'd affect all of the speakers equally. All 8 audio channels are sent over the same wires as the video, during the video's "vertical blanking interval".
Edited to add: I'd check to make sure the subwoofer cable is still tightly seated at both ends and that the cable hasn't been damaged.
Initial subwoofer settings should be with Gain about 50%, LowPass at the highest possible frequency, Phase at 0. During the EzSet/EQ setup, the sub should be on constantly: put the Auto switch in the On position. After EQ has finished, set it to "Auto".
Edited to add:
The EZsetup procedure should complain if it can't detect the subwoofer.
After running the EQ setup, check to make sure all of the speakers are set to be "Small". For the best sound, you should change that setting to "Small" if it is set to "Large". "Small" really means "enable bass management for this speaker". If all the speakers are set to "Large", the sub won't be used for anything but LFE.
Marantz SR7009 avr + MM9000 amp --> Atmos 7.1.4
Fronts=NHT 2.9+AC2, FH+TM=DefTech PM1000, LCR+TM amped