While I don't know the cause of your problem, perhaps I can offer some information that will help you find the answer.
There are two ".stf" files for any given project. The "application.stf" file resides in your application directory.
The "system.stf" file is located in the folder containing your system library. It contains information the system libary and application need for compilation.
Both of these files are actually XML files. I've never seen one become corrupt though. Did you perhaps relocate your application files to a different folder on your computer after creating the project? One of the items found near the top of the "system.stf" file is the location of your SOPC builder generated PTF file.
The "application.stf" file is usually pretty bare. As an example, here is what mine looks like for a specific project:
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<stf>
<project sdk="trio_top_syslib" target="Nios II Application">
</project>
</stf>
Not very interesting as all it does is call out the system library associated with the application.
What the error message is telling you to do is basically wipe out your application and start over. Of course you don't want to lose any source files you've written so you want to copy those over to your new application.
If you can't create a new application without getting this error, then I would suspect and investigate the following in order:
1 - Incomplete software installation. Did you just install the software? Have you rebooted? You may need to check the environment variables to see they were set up properly. Did you install all of the software (IP, Quartus, NIOS IDE)?
2 - Is there something wrong with your SOPC system itself that would feed through into the PTF file? Try creating an application using one of the example systems provided with the installation (
C:\altera\80\nios2eds\examples\verilog). Hope this helps some,
Jake