A friend of mine was leaving to start running as an exercise and I said "Have a good run!". Then I found out it is an idiom with a different meaning. What is the right thing to say in that case?
I would think that in the context of someone actually running, there is no danger of confusion. "Have a good run" is perfectly appropriate for wishing someone do well while running.
I guess if confusion was a real concern, you could say "run well!"