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Well, it seems that you already have implemented a backup plan for this because if the path doesn't exist you revert to the fixed path right? So do the same. Ideally, the build should fail with a descriptive error because I've had many time where I have built something only to scratch my head when the output is missing. Then I realize thet the builder created the entire hierarchy of paths to the build out put in the WRONG location. However, the scenario you describe is a very rare case. Most developers I know work with a source folder NOT a single project file. Moving the project file is bad. Typicaly you would move your project folder. In my example, this is the "subfolder".
The main thing is that NI's definition of relative falls outside the typical understanding. The destination is NOT relative to the project file regardless of how you spin it. It's a non-standard handling. The other option is to allow the user to enter a relative path themselves in the form "..\..\..\builds" and the problem is solved. No sweat of NI's back.