All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad, sallallaahu 'alayhi wa sallam, is His slave and Messenger.
First of all, you have to know that judging a Muslim to be an apostate is a very serious matter. Committing an act of disbelief does not entail judging the doer to be an apostate, for one may be excused for ignorance, coercion, or misinterpretation. Therefore, a Muslim who commits an act of disbelief is not judged to be a disbeliever unless the relevant conditions are met and impediments are eliminated (as specified by scholars).
Muslim jurists differed regarding the acts of worship that a Muslim person has abandoned during his apostasy and whether he is enjoined to make up for them (after reverting to Islam) or not. We shall mention a summary of their statements as cited in Al-Mawsoo‘ah Al-Fiqhiyyah:
Regarding an apostate, the Hanafi and Maaliki scholars held that it is not obligatory on him to make up for the prayers that he had missed during his apostasy, because he was a disbeliever and his belief [reversion to Islam] wipes out this sin (of abandoning the prayer). However, the Shaafi‘i scholars maintained that he is obligated to make up for these prayers after reverting to Islam as a form of strict discipline with him and because he has been obligated to observe this religious duty [performing the obligatory prayers] on account of being a Muslim, so it is not waived on account of his apostasy, as is the case with the rights of other people over him. Abu Is-haaq ibn Shaaqila narrated two opinions on the authority of Ahmad regarding the obligation of making up [for the missed acts of worship] on an apostate:
First opinion: he is not obligated to make up for them ... Accordingly, it is not incumbent on him to make up for what he had missed during his apostasy nor for the period of his adherence to Islam before apostasy. If he had performed Hajj, he is obliged to repeat it because his deeds have been rendered worthless on account of his disbelief.
Second opinion: he is obligated to make up for the acts of worship he had missed during his apostasy and for the period of his adherence to Islam before apostasy; however, he is not obligated to repeat the Hajj, because deeds become worthless only in the case of committing polytheism and dying while adhering to it. Al-Insaaf reads: “If he is an apostate, the correct scholarly view according to our school of Fiqh is that he is required to make up for what he had missed prior to his apostasy but he is not required to make up for what he missed during his apostasy.” [End of Quote]
According to the view that he is required to make up, then he has to perform the missed prayers even at the times when it is forbidden to pray, because it is specifically forbidden to perform voluntary prayers at those times, but the prohibition does not apply to the obligatory prayers. According to scholars, making up for missed prayers has no specific time. He should make up for as many missed prayers as he can, beyond the five daily prayers, at any time of day and night. Sharh Ar-Risaalah by the Maaliki scholar Zarrooq, may Allaah have mercy on him, reads: “A person who is under the obligation to make up for many missed prayers may perform them at any time of day or night, at sunrise or sunset, and with the amount convenient to him without being careless. There is no limit for the number of missed prayers he may perform per day; rather, he should strive in making up for them to the best of his ability.” [End of Quote]
He should make up for the prayers in the prescribed order, because observing order is obligatory according to the majority of the scholars. He should make up for as many missed prayers as he can every day, the least of which is the prayers of two days. The Maaliki scholar Ad-Dusooqi said in his book Haashiyat Ad-Dusooqi: “He has to observe moderation in this regard; it is adequate for him to make up for the missed prayers of two days or more every day but it is not adequate to make up for the missed prayers of one day only per day unless he fears falling short at providing for his dependents were he to make up for the missed prayers of more than one day every day.” [End of Quote]
Allah knows best.