The first d-mail was the one Okabe sent to Daru saying that someone had stabbed Kurisu. In the end, Okabe didn't actually undo that d-mail. Okabe 'transcended' time by allowing time to loop on itself.
This is my train of thought:

Now... to answer your question about the effect of the d-mail: Daru said himself that he thought the first d-mail was just spam and he just ignored it. The first d-mail didn't trigger any significant action in the past when Daru had received it five days prior, and in this sense it's kind of like those few failed attempts where Okabe tried to stop Moeka going to the shrine or when Daru tried to beat Faeris. However, the first d-mail did still have an effect, only the effect of the d-mail was felt
after it was sent. The effect was that Okabe recognised that the d-mail had been sent to the past and he realised the implications of this. It's the
only d-mail that doesn't affect an event in the past relative to the Okabe depicted in the anime; the first d-mail only affects the
future without having any apparent effect on the past relative to the Okabe depicted in the anime.