You may also want to go online with the processor, if you can, and delete all of the blocks that are currently loaded into it.
CLick the SIMATIC Manager's Accessible Nodes button, third from the left or so. In the window that opens, find the folder for the processor (i.e. MPI=2). Open this until you see the blocks, these are the ones currently loaded into the processor. Select All or everything but the System Data Folder, then select Delete from the Edit menu.
If you deleted the System Data Folder you will have to download both the Hardware Configuration and the Blocks.