SWAP EMAC TX RX bits ( MAC <-> PHY )

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Can't you just change the FPGA pin mapping in your project to match the PCB?

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I think we're talking about the HPS EMAC, which is on dedicated pins through the pinmux.

I'd think there is a way to do this by running the EMAC pins to the FPGA, and then back up to the HPS using LoanIO. Then you'd have the pins in the correct place and can rewire them in the FPGA...You might need some management logic, though, and need to use some adaptors in Qsys to turn MII into RGMII?