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 is His slave and Messenger.
If this girl really belongs to the Bohra sect and she believes in their beliefs, then the marriage of your son to her is void (i.e. it should be nullified without divorce) because this sect has beliefs that take a person out of the fold of Islam. For more benefit, please refer to Fatwa 89255.
Moreover, it is not permissible for your son to marry her again as long as she is upon the belief of that sect. If he marries her, he will be committing adultery with her as this is not an Islamic marriage.
Nonetheless, he is excused for what happened in the past if he did not know the Sharee'ah ruling regarding this. If we presume that he had children from that first marriage, they should be traced back to him; Ibn Taymiyyah said: βAll the Muslims agree that every marriage contract in which the husband believes that it is valid is consummated, his children will be traced back to him and they inherit each other according to the agreement of all the Muslims, even if that marriage is void in itself according to the agreement of all the Muslims, and this ruling applies whether the husband is a Muslim or a non-Muslim.β
In any case, if this woman repents from her corrupt belief, then it is permissible for your son to marry her again with a new contract, whether or not we ruled that divorce has taken place, because the first divorce β if we ruled that it has taken place β is counted as only one divorce and it is not an irrevocable divorce with major separation [three divorces]. For more benefit, refer to Fatwa 88502.
Allaah Knows best.