I am creating a game board that will be cut on a cnc machine. It uses a series of circles (peg holes) that are .125 diameter. Is there a way to keep those peg holes the same size when I scale the full project to different size boards?

Theoretical solution: use markers to draw those holes.
Not sure how the cutter will respond, but you can switch off the stroke's scaling with the objects -resulting in the same sized markers.

When you select the whole project, to scale it, deselect the circles/holes. Only the selected objects will be scaled.

However, as I'm trying to imagine what you're doing, I wonder when you scale the rest of the board, whether the circles/holes are supposed to stay where they are? Or is the spacing between them supposed to change relatively?

Let's presume the holes are in a pattern that also needs to scale.

I'd probably go this way:

If the CAM file calls for a drilling operation on the holes, it shouldn't matter... just load the .125 drill.

If the CAM file calls for a profile operation, use clones for the circles in the original size, scale all objects, then change the original circle back to .125 and the clones will follow.

Thanks to all for the great information. I would like the spacing to scale relative to the project, but Tyler, you make a great point on just loading the 1/8 drill and be sure I set it as a drilling operation on my cnc. Lazur - I'm playing with the markers idea, but I'm so new to Inkscape that it's gonna be a bit of a learning curve.