In the following two situations, the EDIF or NGC netlist files are incorrectly deleted:
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Designs that contain partitions and have the XST "Read Cores" or "Cores Search Directories" properties set. A project that contains partitions and has the XST properties Read Cores and Cores Search Directories pointing to edif files corresponding to each partition. Running XST does not generate partition ngc's for these partitions, but only uses the edf's. However, the Project Navigator flow scripts return the EDIF netlists for synthesis and translation and they are incorrectly tagged as generated files in the project. Once this is done, the Cleanup Project Files process deletes these edf files.
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NGC and EDIF files manually copied to a project directory NGC or EDIF files can be manually copied or placed in the project directory to be automatically picked up by NGDBuild. Project Navigator incorrectly assumes that any ".ngc" or ".edn" file in the project directory that has not been added to the project directly, or through association (e.g., IP core added to project), was created by a synthesis or implementation process.
The Cleanup Project Files process deletes these files.
To work around this issue, if you have ".ngc" or ".edn" files that are part of the project design but not added to the project, you can put them in a separate directory and point to them the Translate "Macro Search Path" property.
This problem has been fixed in the latest 10.1 Service Pack available at:
http://www.xilinx.com/support/download/The first service pack containing the fix is 10.1 Service Pack 3.