Say that someone does a good deed like, for example, leading the prayer, and he then apostatizes from Islam and then becomes Muslim again, and then another muslim complements him for his good deed [leading the prayer] and says, "May Allaah reward you," then how should the person who became Muslim again respond? What if he stays quiet, would he be doing anything wrong?

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, sallallahu ‘alayhi wa sallam, is His slave and Messenger.

First of all, you should know that the preponderant view is that when a Muslim apostatizes and then reverts to Islam, the rewards for his past good deeds before apostasy are preserved for him. His good deeds would become worthless only if he dies as a disbeliever. Allah, The Exalted, says (what means): {And whoever of you reverts from his religion (to disbelief) and dies while he is a disbeliever - for those, their deeds have become worthless in this world and the Hereafter, and those are the companions of Hellfire, they will abide therein eternally.} [Quran 2:217]

Hence, this person is still entitled to the rewards of his past good deeds before apostasy. If someone says to him, "May Allah reward you," he should respond by saying the same to him, and if he stays silent, there is no harm on him.

Allah knows best.