I had a flag pole mount that my contractor installed when I had my siding replaced with hardi few years ago. I got some wind and it pulled the mount out from my hardi and has a few holes where the screw for the mount were since the contractor just put it in the harding and not into something hard. What can I use to repair the holes in the hardi?

How big are the holes? Are we talking #8 deck screw sized or thumb sized?

If the latter, caulk and paint it.

They are quarter sized where the screw pulled out

I'd caulk that too and seal it up. Then I'd slap some paint on it. If you want to replace it then you'll need to loosen nails on the lap board or two above the one you are removing so you can raise it enough to get the nails out. It's probably going to break since it's hardie so plan on replacing a few more while you're there.

JB Weld - Water Weld Putty. Sand to match texture if you want then paint it.