Issue occurred during hot sweaty weather and cool torrential rain.
I find this is the worst weather for problems in the shorts area, wet and warm
Ditto that (- well the worst weather for skin damage anyway.)
You say it's the side of your balls and that it's your shorts rubbing.
I would imagine you'd notice it if and when the shorts 'riding up' and do something about it there and then, so are you sure of this?
Could it be an inner leg-conker bag interface issue? (In which case some careful on the bike 'positioning' along with the suggested basting of chamois cream or similar might reduce friction?)
An alternative that hasn't been suggested is turps, i believe some people use it to toughen the skin on their hands, instead of a leather chamois you could get a leather bag