Why does the Intel® Stratix® 10 device not respond to JTAG status after reconfiguration with a bitstream with the “Run configuration CPU from internal oscillator” option selected?

Due to a problem in the Intel® Quartus® Prime Pro Edition Software version 21.1 and patch 0.06, you may see that the Intel® Stratix® 10 device no longer responds to JTAG status commands after a bitstream reconfiguration with the option "Run configuration CPU from internal oscillator" enabled when the previous bitstream had external oscillator enabled.

To work around this problem, perform a power-on reset (POR).

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