compiling speed-a few ?

[Greg McKaskle]

This shouldn't do any harm. The shadow will be in memory on the cRIO, and your Main VI too. The big benefit is that if you Main VI is removed from memory, the 500 or so other VIs that it references won't need to be redownloaded because the shadow will keep them there. I have never seen an issue with using this trick. If you think you see something funny, just close the shadow occasionally.

Greg McKaksle

[Chaos in a Can]

You should be able to use the calibration file idea without running into the aforementioned problem.
You could load your main project that uses the calibration file as the startup application, then use a button on the front panel of a vi to save the current settings to the calibration file. Running the debug version should allow you to change the calibration file without rebuilding the startup application.