That does not invalidate the "argument" in any way, since mysterious ways include the sucky world, and in any case, it is all just a "test".
I think Luke is more an expert on the subject, but I think William Rowe's argument ( on luke's old site ) covers the "mysterious ways" quite well. I remember William Craig trying to come up with a terrible argument about animals not feeling "proper" pain to try to circumvent the problem.
Let's wait for the true expert to step in, though ;)
These are written from the angle that Christians deconverting is bad.
Cognitive reasons
Breaking up because a relationship with God becomes unworkable
Leaving because other Christians aren't empathetic about doubt
At what age do people leave?
It looks as though there may be more articles in the series.