Thanks winsmen, this is the only workaround that solved the problem on my system.
This is a recurring issue I face with S32DS 3.5. In the past it seemed to eventually resolve itself after some time (perhaps Windows or antivirus policy updates), however on this occasion I had urgent work to do and I could not force it to function via system shutdown/restart or the autorebase.bat script.
Here is the exact procedure I used:
- Open project properties in S32DS.
- Presently this needs to be done for all projects that are affected (which is anything built in S32DS managed make context).
- Expand C/C++ Build and select Environment.
- Select the PATH variable and click the Edit... button.
- Pre-pend the path to external directory (outside of S32DS installation) containing make.exe, for example I installed a separate instance of msys64 which includes make.exe at the default path of: C:\msys64\usr\bin.

- Click OK then Apply and Close.
- Attempt to repeat the build or clean operation and it should now work.
I tried to apply this workaround at S32DS workspace level by defining the PATH variable in Window -> Preferences -> C/C++ -> Build -> Environment but this does not work. It only seems to support appending of environment variables to the project-local environment, meaning the non-functional S32DS make.exe will supersede the external instance and be invoked first leading to the error. I will update this thread if I find a way to apply the workaround in a general way.
Best regards,
Gary