SW4STM32 and SW4Linux fully supports the STM32MP1 asymmetric multicore Cortex/A7+M4 MPUs

   With System Workbench for Linux, Embedded Linux on the STM32MP1 family of MPUs from ST was never as simple to build and maintain, even for newcomers in the Linux world.
And, if you install System Workbench for Linux in System Workbench for STM32 you can seamlessly develop and debug asymmetric applications running partly on Linux, partly on the Cortex-M4.
You can get more information from the ac6-tools website and download two short videos (registration required) highlighting:

System Workbench for STM32

Updating a STM32FCubeMX project after modification

This is what I have figured out so far. It seems to work.

Before generating new code from CubeMX.

Copy the SW4STM32 Directory
Generate new CubeMX code
Delete the SW4STM32 Directory created by CubeMX
Rename or Copy the original Directory back to SW4STM32
Go into the Project Explorer in Eclipse (OpenSTM32) and Refresh the Project (F5).

The project now compiles with the original files and settings.