Well 11 months later the Sony TV with the brand new motherboard has now lost use of all the 4 HDMI sockets. I can only ascertain that the PS4 has wiped out the EDID eprom again, I'd say it's not limited to just the 2.0 OS.
To replace the TV motherboard again is not worth it on a 6 year old TV, so I have added in my HDFury HDMI Doctor inline from the PS4 to TV and I get sound and vision again as it fakes the EDID.
My advice to you all, if you have experienced this issue with one TV, then make sure you don't migrate your PS4 to you new TV unless you have some kind of device between them or you risk wiping out the EDID settings on that one also.