Hi,
Your issue looks similar like below known issue.
Due to a problem in the Intel® Quartus® Prime Pro Edition Software version 19.3, you may see a design link error in the EMIF Toolkit with the following message:
"An error occured while linking the project to the device"
Once a programming .sof file is linked through the "Link Project to Device" step in the EMIF Toolkit, and then unlinked through the "Unlink Project from Device" step, the same programming .sof file can't be re-linked through the "Link Project to Device" step again. If this is required, you will need to close the EMIF Toolkit and then re-open it.
Can you confirm and try out the workaround which is similar to Steve's suggestion as well.
The other possibility is to reduce JTAG frequency from default 16MHZ to maybe 16MHz or even 6MHz
Also you can try to create EMIF example design with just one EMIF interface to test out EMIF toolkit to help rule out is it Quartus design issue or board JTAG issue.
Thanks.
Regards,
dlim