I have the same issue on Arch Linux (Antergos actually) kernel
4.4.43-1-lts.

Just wanted to add my workaround:
 
user@arch>$ sudo ethtool -s enp4s0f2 duplex full
Cannot advertise duplex full

And it usually works again. Sometimes I have to add the following too because 
it's not always enough:
 
user@arch>$ sudo ethtool -s enp4s0f2 duplex half
Cannot advertise duplex half

I suppose this should be reported to whoever wrote the r8169 driver
(thanks to them by the way!), not here. Hope that helps.

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https://bugs.launchpad.net/bugs/771857

Title:
  Realtek 8168B (r8169) interface not working following suspend

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