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.