After trying this out, I tracked down the true source of my troubles. I was having issues doing the update, which led me to look more at my own network. For some reason, DHCP is handing an address to the LinkStation that is already being used on an IP phone.
I did need to use that special debug menu to reset the IP though. The tool on the standard Buffalo NAS Navigator to change IP's wouldn't do it.
I'm considering it fixed, or least able to work around. Still not sure what's allowing the LinkStation to get an already assigned IP though.
Thanks for your help!