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The program generated is not compatible with any of the CPUs in your target configuration.

I found similar posts for this error dialog.   I found an answer for my own environment...

I am using CCS 5.5 targeting a group of Tiva targets.

Every so often, I have to blow away my CCS workspace's .metadata directory as it gets fouled up.  Symptoms of fouling are:

  1. The ctrl-space auto completion help stops working or gives non-sensical suggestions
  2. Finding all references either does not find any references and you are sitting there looking at one, or it finds some but navigation to the reference puts you in an applicable file, but at the wrong line
  3. Compiling dependent projects occurs and all files are rebuilt, even though a build is not required.

So I blow away .metadata and then use a batch file to rebuild the workspace using lines such as...

C:\ti\ccsv5\eclipse\eclipsec -noSplash -data C:\Data\Code\CCS -application com.ti.ccstudio.apps.projectImport -ccs.location C:\Data\Code\LM4FCommon\CommonApp\trunk\ccs

Then I get the message in the title. 

To fix, for the project I go into

Properties -> General -> Main

and find that the Connection to my emulator is now blank.  I reselect "Manage the project's ... " option.  And then reselect the emulator.

This action then creates a new <target chip>_startup_css.c file.  Delete this as it confuses the project with multiple definitions.

Now you are ready to go again.

Perhaps the problem is that over the CCS versions, the default startup_css file name has been changed or it is the fact that I name my <project>.ccxml file after the project and not the chip that confuses CCS.

I hope a TI CCS engineer picks this up as a repeatable way to foul a project and then figures out what is broken in CCS.

It is almost as if a project file has a field for the version of CCS which is not updated as needed.  When you re-import a project, CCS updates that project file, thinking a new version of CCS is being used.  It then converts the project file needlessly.  It is the conversion that has an error in it and it blows away the section of file concerning the connection.