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I have basically the same issue. Being able to have several .cydwr files in a project, and selecting which one is "active", would be ideal.
If there is no way to do that, what is the closest you can get? How would i set up my project(s) to make two different builds which have identical source code AND schematic, but different pinouts? Sharing source code between two projects works fine, but can I also share a schematic?