A person's Aqeedah is wrong, but he does so much good work. How does Allah compensate for his good work?

The Prophet (ﷺ)

“…None will enter Paradise but a Muslim, and Allah may support this religion (Islam) even with a Fajir wrongdoer.”[1]

Look at Mother Theresa for example, she did a lot to help the poor and sick, but what she called to is incorrect. So we don’t judge people only by their good deeds. Allah's attribute of Ar-Rahman Ar-Rahim reaches all His creations in this world, but in the Hereafter His attribute Ar-Rahim is only for the believers.

If one's creed is wrong or one is a disbeliever, the good deeds are compensated by the ni'mah bounty of Allah in this life, but there is nothing for them in the Hereafter.  As for muslims, even though they may have faulty Aqeedah, we ask Allah (سبحانهُ وتعالى) to forgive them. Even scholars may be afflicted. For example, the great scholar Ibn Hajar Al-Asqalani, his beliefs was influenced by the Zaidiyah teachers he took knowledge from. However, later when he met other scholars, he corrected himself. There were other scholars like Imam as-Suyuthi.

Our approach in such situations is to ask Allah’s forgiveness for them. And Allah knows best.

Reference:

[1] [Sahih al-Bukhari 3062 Vol. 4, Book 52, Hadith 296]