thanks for the report!
This is a known issue logged as S32DS-4629.
Engineering team is currently working on the fix, which should be able in the next release/update.
Please delete the output directory to force your project rebuilding.
I tested couple projects - and in my case are .o and .elf files deleted after clean. In your case - it is related to one particular project or for all of them? You can try to delete project's Debug directory. Other workaround may be create new workspace and import there your existing project.