Is there a known issue when migrating an IOPLL Intel® FPGA IP iopll.ip file to Intel Quartus® Prime Pro Edition Software version 18.0 or 18.1?

Yes, when migrating an IOPLL Intel® FPGA IP iopll.ip file generated for Intel Cyclone® 10 GX, Intel® Arria® 10, or Intel®Stratix® 10 devices in a previous version of Intel Quartus® Prime Pro Edition Software to Intel Quartus Prime Pro version 18.0 or later, the IOPLL auto-reset settings will fall back to default state during automatic IP upgrade. 

To work around this problem, the IOPLL Intel® FPGA IP auto-reset setting needs to be re-enabled, and the iopll.ip file regenerated manually during IP migration.

This is scheduled to be fixed in a future release of the Intel Quartus® Prime Pro Edition Software.