It was CPU change that prompted PCI-E Link Speed “disappearing” but not because CPU is a problem but BIOS for 5600X hasn’t exposed PCI-E Link because they motherboard manufacturer relies on AMD AMI for handling. In other words not exposed.
I put 1600 into the motherboard and saw “Force PCI-E gen” but unfortunately I think the support for 1600 is lacking, even though gen speed is exposed, where as 5600X probably has stellar support (has PBO, undervolt, and alot other settings in BIOS) but is a road block for GPU riser use without PCI-E Link speed option. The rationale is if the motherboard’s max speed is PCIE 3.0, other option is 1.0, then it will run at 3.0 even without PCI-E Link Speed forcing but I will have to inspect that at a later time. Most people assumed, even for brand motherboards, that if PCIE link is set to AUTO then it will work just fine by itself right? Wrong. Risers require forcing of gen 3 or gen 4 or there will be issues. So who is to say that this motherboard, for 5600X, is giving riser PCI 3.0 and not 1.0 connection?