Hi Karl,
can you provide detailed instructions to reproduce this? If I create Unnamed1, Unnamed2 as in your example and switch back to Unnamed1, all projects still seem to work. Do you maybe have enabled the "System window embed" preference and dropped a transcript from one of the projects into another one? Maybe you can debug the issue by inspecting "Project transcript" and the model of the transcript window in question. They should point to the same instance.
Best,
Christoph