Due to a problem in the Quartus® II software, you cannot route I2C_EMAC ports of Intel® Arria® 10 SoC HPS to the FPGA without enabling the EMAC modules when you use them as ordinary I2C ports.
To work around this problem, open the Platform Designer project file (.qsys) in a text editor and find the following lines:
<parameter name="I2CEMAC0_Mode" value="N/A" />
<parameter name="I2CEMAC0_PinMuxing" value="Unused" />
<parameter name="I2CEMAC1_Mode" value="N/A" />
<parameter name="I2CEMAC1_PinMuxing" value="Unused" />
<parameter name="I2CEMAC2_Mode" value="N/A" />
<parameter name="I2CEMAC2_PinMuxing" value="Unused" />
Then edit the lines of I2C_EMAC you want to route to the FPGA as follows. In this case only I2C_EMAC0 and I2C_EMAC1 are routed to the FPGA.
<parameter name="I2CEMAC0_Mode" value="default" />
<parameter name="I2CEMAC0_PinMuxing" value="FPGA" />
<parameter name="I2CEMAC1_Mode" value="default" />
<parameter name="I2CEMAC1_PinMuxing" value="FPGA" />
<parameter name="I2CEMAC2_Mode" value="N/A" />
<parameter name="I2CEMAC2_PinMuxing" value="Unused" />
Open your qsys file and you can find I2C_EMAC I/O in the HPS module. Make sure that after you open the HPS parameters window and edit any pin settings, the settings above may disappear.
This problem is scheduled to be fixed in a future release of the Quartus II software.