I just had an experience that I thought I would comment on, not because it is new, but because though it has happened enough in the past it gave me a minute of pause and I decided to write about it.
It goes like this: You pray for someone/something you said you would or that you had on your heart, and felt confidence on all counts (faith, scriptural support, heart fervency, etc) – all those things that a person who prays knows as basis for faith that God hears, and answers. Then, the very thing prayed for seems to suffer some sort of attack that creates some doubt. Did God hear? am I disqualified for some reason? what is going on?
In this instance I prayed for some people in missions, and my daughter specifically, to be protected particularly in traffic. Whether simultaneously or soon after a report of a serious accident. So, what is going on here? Did this prayer not work or did it work, but in a flawed way. Some people are not going to like the phrasing “prayer working”, but we labor in our prayers, so it seems like a good way to think about this. And James speaks of effectual prayers, effectual meaning “producing an intended effect”.
While there might be numerous explanations, one that ought to be considered, when a seemingly opposite situation seems to come forward than the one prayed for, is that you have walked into enemy territory. You have started to wage war spiritually. Sometimes the enemy of our souls is used to having dominion over an area, of life, of a family, of a city or nation, and the prayer of a fervent saint is making an inroad of uncomfortable efficacy to take back blessing for the situation prayed for.
You may be experiencing the resistance of a an evil spiritual power. That is one possibility that you should consider. I believe the Spirit of God can give you insight into whether this is the case in your particular request. There are times when Jesus said we should be encouraged when we see seemingly hostile events taking place.
In the case of my own prayer, the lives of the people in that accident were kept, even though there was injury. My daughter was not involved though some of her coworkers were. What does this tell me? It tells me that in an area that desperately needs the blessings and freedom of the gospel, prayer for mission workers should be redoubled. That is right- I am encouraged to further pray for protection… to meet resistance with faith in the power of the covenant in Jesus blood. And therein is the key to prayer that works. God honors His covenant in the blood of Jesus. It is our confidence in that that the devil fears, and the enemy of our souls will try to squelch. The gospel (good news) of freedom is the news that a covenant, an everlasting agreement, has been given to us and sealed with the blood of God’s only begotten son. The psalm 91 promises of protection and deliverance are ours in Christ Jesus. When we know that God is pleased to answer us, then our prayer will “work”. Although it is more accurate to say that we know that God is going to act on our behalf.
I encourage you to pray, and to find what is promised you in the eternal covenant in Christ Jesus for us.