In the Intel® Quartus® Prime Pro Edition Software version 20.2 and later, the EMIF Debug Toolkit can support multiple EMIF Interfaces in the same or different rows by following the guidelines in the "Configuring a Design to Use the Toolkit" section in the External Memory Interfaces Intel® Agilex® FPGA IP User Guide.
In addition, ensure that all the IPs are added into one single .qsys file.
Note: USB-Blaster II should be used when you try to use the EMIF Debug Toolkit.