Sometimes changes to the microcontroller are made and you need to generate new code from STM32CubeMX. To keep the USER CODE in for example main.c the following steps should be followed.

1. Make your changes in the .ioc file
2. Move the main.c file of the board you are working from Core/Src/[board] to Core/Src files.
3. Generate code
4. Move the files back to their original location

For the other generated files like syscalls.c and stm32[version] can be copied pasted into the correct location, replacing the old files.