First off, it will be impossible to match the existing agregate. However, you may be able to use some new agregate rock (check with the local landscape dealer) and epoxy it into the holes. Then seal the whole deck to protect from getting water under the stones where it can freeze and pop them off.
Another, more drastic method, would be to saw the affected part out in a square or diamond shape, break it out and replace the concrete with new agregate based concrete. It may even be available in SackRete.
Caution, placing concrete less than 2" thick will break up and pop off.