Ihave a project that was created using Partial Reconfiguration in the 13.1 software.
In the Design Runs window, I reset two out of three runs and tried to run one of them.
Then, the fatal error message appears.
To work aroundthe issue,make sure that you have the netlist design as well as the implemented design closed before you make changes to your design runs or before launching them.
This issue is fixed in the 13.2 PlanAhead tool.