Why does the In-System Sources and Probes Editor of Intel® Quartus® Prime software not recognize the instances I want to use, when multiple devices with In-System Sources and Probes IP are in the same JTAG chain?

When multiple FPGA or/and CPLD devices are in the same JTAG chain and they have one or more In-System Source and Probe IP instances respectively, the In-System Source and Probe Editor of Intel® Quartus® Prime software may not recognize the instances of In-System Source and Probe for the device 
you want to use and Unexpected JTAG communication error may be displayed in the status of the instance list in the Instance Manager pane.

This is because the In-System Source and Probe Editor recognizes the instances of the first device in the JTAG chain just after scanning the JTAG chain.  So you need to select your target device and update the list of instances for the device in the Instance Manager pane.

To display the instances of In-System Source and Probe for the device you want to use, follow the procedure below.

1. Select a device you want to use the In-System Source and Probe from Device in the JTAG Chain Configuration pane.
2. Execute Recreate Instances From JTAG Device from Edit menu. Then the list of instances in the Instance Manager pane will be updated for the device selected.