Hello
You can ask the debugger to preserve content of some FLASH or EEPROM memory using FLASH AEFSKIPERASE command.
This command is explained in the {Install}\Help\PDF\Debugger_HC12.pdf manual, chapter "Book IV Commands and Environment Variables" section "Connection Specific Commands" -> "NVMC Commands" -> FLASH
You can also find some information in the {Install}\Release_Notes\HC12\Notes_debugger_P&E_Multilink_Cyclone_Pro.txt file.
Be careful, there are only a couple of flash block that can be programmed/erased separately. THe debugger flash programmer does not allow you to arbitrary erase/program any block of memory.
Please use command FLASH to see a list of the blocks that can be programmed/erased separately.
Another approach to do so is to merge the second application code inside of the code from the first application and program both applications at once.
This can be done using the command HEXFILE in your linker parameter file. Please refer to the Build_Tools_Utilities.pdf manual for information on this command.
CrasyCat