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Tom said to mention this here on behalf of technical support. When exporting native text MODFLOW files, the files are not updated with new information. For example put new information into the MODFLOW | Global Options | Optional Packages | RCH package and click OK. Unless the project is manually saved after making the edit and before exporting the native text file those changes aren't saved, but users may not realize clicking OK doesn't update the files. It may be helpful for the user to receive a reminder that 'You have not yet saved your changes to the model. Would you like to save these changes before exporting the native files?' or something along those lines.