SmartFusion debug problems
Did you recompile the ARM code for the new package? Additionally, did you incorporate the newly generated library from Libero into your SoftConsole project? This may have all been automatic for you if you're using the standard design flow. The A2F500 may have more memory/flash than the A2F200 and it could affect the memory map.

I have only used the SmartFusion 2 which is a different animal, but my understanding is the design flows in Libero and SoftConsole are similar. I would explicitly regenerate the output source files from Libero and make sure they are the ones referenced in SoftConsole and be sure to do a full rebuild there. There also may be linker changes required if the memory map does change.