You might observe the above error message while trying to link the project to a device using the UniPHY External Memory Interface (EMIF) Debug Toolkit. This problem may be observed, if you have the .jdi file located in a directory other than the project directory. For example, if you have the .jdi file placed in <project directory>\SubDirectory, you might get this error.
To resolve this problem, move the .jdi file to the main project directory.
This problem is fixed starting with the Quartus® II software version 12.1.