Hello,
I did not write PE cannot work with single elf in multi-core project. I wrote, S32DS does not support this option and this could causes the issues.
Also, please compare the price of Lauterbach Debugger and PeMicro debugger. Even more, Lauterbach uses Trace32 software, which is on the different level than debugger used in S32DS which is provided free.
But maybe you can try contact PeMicro support and ask them, if they can help you to resolve this problem, because whole debugger integrated in S32DS is provided by PeMicro.
Regards,
Martin