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When debugging an application from flash, you want to let the application boot in its normal manner. If you select "load program" in CCS then you are overwriting the application that loaded from flash and not debugging the code as it runs normally. You should instead do "load symbols" in CCS and then select your .out file. This will allow you to debug your code using variable/function names without overwriting the code that boots from the flash.
CCS 3.3: Go to File -> Load Symbols -> Load Symbols Only
CCS 4.x: Right-click on the project and select Debug Options. On the "Debugger" tab choose "Load Symbols" instead of "Load Program"
CCS 5.x: In the "Debug View" tab choose "Run"--> "Load" --> "Load Symbols"
