There was a technical issue, we were able to see your post until today. We're sorry.
Could please tell us the platform and the OS you're using?
We'll continue working in your case, and waiting for your update.
We have received feedback from our engineers.
Please refer to section 220.127.116.11.7 Internal PHY Power-Down State in the Intel® Ethernet Controller I350 Datasheet, and also section 6.2.21 Software Defined Pins Control (LAN Base Address + Offset 0x20).
The following register values:
0x0c0c -> disables PCI + management.
0x040c -> disables PCI, management may still operate.
In terms of eeupdate:
Disable port 0 : eeupdate /nic=1 /ww=0x20 0x040c
Disable port 1 : eeupdate /nic=1 /ww=0xa0 0x0c0c
Disable port 2 : eeupdate /nic=1 /ww=0xe0 0x0c0c
Disable port 3 : eeupdate /nic=1 /ww=0x120 0x0c0c
You can try it on port 0, but it's doubtful that it'll work.
According to the datasheet this port can't be disabled to avoid a bricked EEPROM.
Please let us know your results.