If a man has promised a lady to get married of her and they got engaged. Then a misunderstanding happened between him and her father. Due to the misunderstanding they kept away from each other because they don't know if they are going to get married or not, But they love each other.
After 10 months he made a relation with an other woman and he prayed "Salat Al Istikharah" to marry her in case if she will be the best wife for him, because Allah knows best. He asked Allah to make his marriage from her easy if she is the best wife for him. Then she asked him to marry her in a secret way without telling any one else and she convinced him that it is legal in Islam. He married her as she asked him but at the same time the previous lady was still in his heart and he love her. After months he found that the way of their marriage is not accepted in Islam.
The first thing in this question is that he prayed “Salat Al Istikharah” to get a help from Allah in what he is going to do, but he married her in a wrong way and the marriage now is revoked. What's that mean?
The second thing he still love the previous lady even if they are away from each other and can't see each other. In addition to that he promised her to get married and they are engaged.
In this case, which one he has to marry and why?

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 is His slave and Messenger.

The Istikhaarah is Islamically desirable and its result is known by the comfort and content that one feels in his heart and the matter being facilitated. However, it might be that the matter is not clear for the person who performed the Istikhaarah as he is too much driven by his desires or very attached to the matter. Also, a person may perform the Istikhaarah on a given matter and the matter is facilitated for him, but he is soon repelled from it or that he faces some problems.

Nonetheless, he should firmly believe that Allah does not choose for him except that which is good for him. In fact, a calamity may sometimes be better for a person as Allah expiates some of his sins and elevates his status, and so forth.

As regards the secret marriage which you mentioned in the question, then we do not know how it took place. If the marriage took place with the consent of the woman's guardian and in the presence of two witnesses, then it is a valid marriage even if other people are not aware of it. However, if it took place without the consent of the guardian, then it is an invalid marriage.

On the other hand, if the problems between you and the first girl's father are getting worse, and there is no hope for reconciliation, then you should not continue to be attached to that girl. Rather, you should put the matter in the Hands of Allah and ask Him to bless you with a pious wife. It might be that it is not good for you to marry her, and it is for this reason that Allah kept her away from you.

Finally, we advise you to repent to Allah and ask His forgiveness for your previous marriage if it took place in a prohibited manner.

You should also perform Istikhaarah and seek advice about marrying the first or the second woman.

May Allah guide us all to what He loves and He is pleased with.

Allah knows best.