Tell him you would really appreciate if he would talk to his sons to let them know to use extra care when they are retrieving a ball that lands in your plant areas.
I would not ask him to switch spots with the kids because he might take offense to that. (he might think you see his children as irresponsible)
If the father is sympathetic to your request then he will talk to his boys or he will switch “spots” with the boys on his own.
I also have my own problem with a neighbor - but he is a total jac@ss. His water well sits on the property line. His water well is leaking a bunch of water into the corner of my yard. This has drown and killed one of our full grown Forsytha bushes and the water now is making a 10' plus long rut in our yard. We have asked him to numerous times to please repair his well but he ignores our request. The next step is for us to get a lawyer involved because if he keeps ignoring it the damage to our yard is going to be costly and we should not have to pay for it. The problem is it is senseless to repair our yard until he repairs his leaking well. (We live in the rural country BTW)
You should consider digging a trench that would re-route the leak away from your property and then get the repairs done. Find out who his insurance company is and file a claim against his liability coverage. Try to do that before doing the repairs, though you could re-route to protect your property from further damage.