Chisel out the damaged mortar at the joint under an end cap.
Continue to chisel off the mortar under the cap until it loosens. Remove the end cap.
Remove any loose mortar exposed by taking off the end cap.
Take off the rest of the caps on the row just as you did the first one.
Smooth out the mortar on the top row with the hammer and chisel.
Measure the dimensions of your wall. Obtain flagstone caps that will overhang the wall by 1/4 inch. This helps prevent moisture damage.
Obtain premixed mortar and place the contents of a bag in a wheelbarrow. Add the recommended amount of water and stir with a hoe.
Place a small amount of mortar on the mortarboard. Scoop enough mortar off with a trowel to make a 1-inch layer over the base for the end cap.
Spread the mortar on the wall. Center the flagstone end cap on the mortar bed and press down. Continue to press until the mortar bed is about 3/8 inch thick. Trim off excess mortar with the trowel. Ensure that the cap overhangs the wall by 3/4 inch on the sides.
Install the rest of the caps on the row as you did the first. Cut the last cap to fit with a hammer and chisel, if you only need a half-sized stone. Keep in mind that most walls are built by staggering the rows, so one end is likely to contain a partial block or stone.