Dear @abelton,
Could you check trying a Hardware reset by writing 0x1 to register 1E.2681 on AQR113C via MDIO to see if it recovers it from a bad state.
Please see Orin can not read the PHY reg data - #15 by WayneWWW and try
if phytool write mgbe1_0/0:0x1e/0x2681 0x1 helps?