No action is required for Libero SoC.
I/O Editor Above DDR The pin assignment is fixed and customers cannot change the DQ bit.

PolarFire Family Memory Controller User Guide
"Tip: DQ bit swapping within a byte lane is supported on the PCB between the Fabric DDR controller and DDR3, DDR3L, LPDDR3, and DDR4 memories for routing flexibility.”
As stated, please perform hardware bit swapping on the board.

The PolarFire Family Memory Controller User Guide can be found under the User Guides tab in the Documentation section.
https://www.microchip.com/en-us/products/fpgas-and-plds/fpgas/polarfire-fpgas/polarfire-mid-range-fpgas#Documentation