All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad, sallallaahu ‘alayhi wa sallam, is His Slave and Messenger.
First of all, we say that the majority of scholars held that following the sequence is a condition for the validity of stoning the Jamaraat. The Hanafis, however, held that following the sequence is an act of Sunnah, not a condition for validity.
Ibn Qudaamah said: "Sequence in stoning the Jamaraat is an obligation, according to what we have mentioned. If the pilgrim fails to follow this sequence and begins with the Jamrah Al-‘Aqabah (the third, the largest), and then the second (the middle), and then the first (the smallest), or begins with the second, and then the other two, then only the stoning of the first Jamrah counts and he is obliged to repeat the second and third; (Imaam) Ahmad stated that. And if the pilgrim stones the third and then the first and then the second, then he is obliged to repeat the stoning of the third only. This is the opinion of (Imaam) Maalik and (Imaam) Ash-Shaafi‘i ... Al-Hasan and ‘Ataa’ said that following the order is not obligatory, and this is also the opinion of (Imaam) Abu Haneefah who said that if the pilgrim does not follow the sequence in the stoning of the Jamaraat, he should repeat the stoning of them in the correct order; however, if he does not, it is sufficient for him and the rite is valid." [Al-Mughni]
One of the reported opinions of Imaam Ahmad is that stoning the Jamaraat in the correct order is an act of Sunnah (and not an obligation) and another opinion is that failure to observe the order is pardoned in case of ignorance. Al-Mardaawi said with regard to failure to observe the order in throwing the pebbles: "If the pilgrim fails to stone the Jamaraat in sequence, it is not sufficient for him (and he has to repeat the stoning of them in the correct sequence); another reported opinion from (Imaam Ahmad) is that it is sufficient for him in all cases; and a third opinion is that it is sufficient for him only in case of ignorance." [Al-Insaaf]
Based on the opinion that following the order is a condition for the validity of stoning the Jamaraat, if the pilgrim stones the second Jamrah, and then the first and then the third, as the case in the question, then only the stoning of the first one counts and the other two do not count. Therefore, he is obliged to repeat the stoning of the second and third. If he does not, then he has to offer Dam (animal sacrifice) for missing the stoning of more than three pebbles. This is the opinion of Ahmad and Ash-Shaafi‘i and it is also the opinion we adopt at Islamweb.
The Kuwaiti Encyclopedia of Jurisprudence (Al-Mawsoo‘ah Al-Fiqhiyyah) reads: "The view of the Shaafi‘is and Hanbalis is that a sacrifice is due on the pilgrim who misses the rite of stoning as a whole or misses the stoning on one or two days or misses throwing three pebbles in any of the three Jamaraat."
One is not obliged to offer more than one animal sacrifice if one has thrown six pebbles in one of the Jamaraat because one has to offer a sacrifice only if one misses three pebbles or more, whether he missed them in one Jamrah or two or all three of them, because the expiation concerning the stoning is not divisible. The Shaafi‘i book Tuhfat Al-Muhtaaj reads: "The scholarly opinion according to the Shaafi‘i School is that the pilgrim is obliged to offer an animal sacrifice for missing three pebbles or more, even if by more we mean missing the rite of throwing as a whole; this is because it cannot be divided into parts as with shaving the head."
Shaykh Ibn ‘Uthaymeen said regarding the pilgrim who missed the throwing, "It is incumbent on him to offer an animal sacrifice whether he misses throwing the pebbles on one or all days or fails to stone any of the Jamaraat (the first, second or third). The judgment applies to all these cases because the expiation concerning the stoning is not divisible."
Allaah Knows best.