The datasheet for the HCS08 controllers has the information and sequence spelled out in the FLASH memory section of the document (for example, reference MC9S08AC60 datasheet Page 52). To write those registers and flash memory locations using Background Debug Mode connection, reference AN3335 document that explains the commands available, which will have read and write commands to use with the appropriate flash controller reg addresses to erase the flash blocks. Depending on your device, you may have to erase multiple blocks separately, I think.