The challenge levels themselves irk because they are now retrofitted to justify shooting more than one probe. You could make it so the stock replenishes slowly on its own, so that if you are careful you never run out, but still have a 'fail' state if you are ham-fisted.
Or. if you had one probe that scanned everything based on its context (so shot into a planet you scan surfaces, shot past asteroids you get minerals, shot into space you reveal POIs) it would make more sense. Forget this 'I'll name that tune in three, Lionel' probe challenge, remove the infinity symbol and just give the game a tool that is multifunctional and invisible. One probe launch for one job. Engineering could then be used to increase the probes range, scan radius etc and then you have no grind of having to fire multiple probes.
Are you encouraging exploration and using the mechanic, or are you trying to limit it out of the belief that of all the things the game could possibly focus on - its probes? I mean I get it. But really if we take that to its logical conclusion then we have to approach pulse lasers and a bunch of other stuff and I reckon theres better use of Frontiers time.
People are going to do this hundreds of times. I will be doing this, potentially, hundreds of times, not once or twice; so no, it stops being a challenge and ends up a chore, if i am having to stop everything, repeatedly to sort out the probe situation.
Theres still value in learning the trick. It may save time, and has value in doing so, versus spamming. Dont underestimate the value of that.
Because we, the community at large, will be doing this a lot. Not just once or twice, on Sundays.