scltn
This is not the cheapest solution.
Assuming the milling is in advance of new ACP placement, and most of the stone base is in good enough shape to place new ACP on.
Assuming these areas are too small to get motorized equipment ( to rework base course )into.
Patching small areas of a base course is not very productive/successful due to the inability to achieve a good compactive effort in small areas.
Excavate the bad base out to neat *lines and place a base ACP ( *minimum size for small steel wheel compactor )flush with top of stone base. Then lay your surface course over the patches and existing base. 8-12" should be more than sufficient depending on your subgrade condition.
Obviously you may have to dry these patch areas out if they are unstable, pryor to placing the patching ACP.
Good luck