This issue is manifested in two different ways, as follows:
Changing TopIf a process is run on a source file at the root of the hierarchy and then the top-level module is changed to another source that has a different hierarchical root than the first, the status of the project is not correctly reset. Consequently, subsequent processes will likely fail since the initial processes were run on the first source but subsequent processes are looking for files created for the second source. One common error that occurs in this case is the following:
"ERROR:HierarchicalDesignC - Could not find Partition for hierarchy node </<first_top>>. HDProject not loaded."
To work around this issue, either select the re-run all option for a process or select Project -> Cleanup Project Files.
Design Errors in Unrelated ModulesWhen a simulation process is run, all schematic sources in the simulation view are processed regardless of whether they are part of the hierarchy currently selected. If there is an error in one of these unrelated schematic files, the simulation process fails.
To work around this problem, the error in the schematic must be fixed or the schematic source should be removed from the simulation view.
This problem has been fixed in the latest 8.2i Service Pack available at:
http://www.xilinx.com/xlnx/xil_sw_updates_home.jspThe first service pack containing the fix is 8.2i Service Pack 2.