Hello christophertschappatt,
thank you for the question.
Because there were some structure changes between KSDK 1.1 and KSDK 1.2, I recommend work separately with these files (e.g. for KSDK 1.1 use KDS 2.0 and for KSDK 1.2 use KDS 3.0), because hand in hand goes KDS release and its MCU support.
Please, keep in mind that for every KDS release you need separate workspace and installed Eclipse updates.
If you have larger project, it is better to migrate it by this way, I attach you a procedure.
I hope this helps,
Best Regards,
Iva