The Intel® Stratix® 10 FPGA IOPLL is not being able to obtain lock when the input refclk is driven by an output clock from the Intel Stratix 10 FPGA E-Tile.
You must perform user recalibration of the IOPLL after the output clocks from the Intel Stratix 10 FPGA E-Tile are stable.
Holding the Intel Stratix 10 FPGA IOPLL in reset until output clocks from the Intel Stratix 10 FPGA E-Tile are stable or pulsing the reset after the output clocks are stable will not resolve the Intel Stratix IOPLL unlocked state.