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