If I am reading this correctly, you are attempting to use a PCIe I/O interface card (the Decklink) with a newMacPro that does not support PCIe, but seems to be dedicated to being Thunderbolt-only. In the Configuration guide for Resolve 11, which focuses on the use of the newMacPro, you will note that the recommended output interface is the Thunderbolt based external UltraStudio 4K.
How are you interfacing to the expansion chassis?
I was not aware that a Decklink would function correctly in an expansion chassis -- seems that the architecture is designed to support storage interfaces, RedRocket and *some* other cards. If you can get the Decklink to function in the expansion chassis, I would simply feed the Flanders from the SDI output. Nothing else would need to be configured, but even with the older MacPros, Decklinks were always advised to be installed in Slot 3 and not in the expander.
"I always pass on free advice -- its never of any use to me" Oscar Wilde.