If God is God then his human creatures shouldn’t be surprised that he isn’t completely comprehensible. So when the Bible says that he is sovereign and does whatever he wants but also that he genuinely engages his people in conversation in prayer and adjusts what he does based on their requests, the argument that this is necessarily a contradiction because we can’t understand how it works is illegitimate.
It seems strange to us that God could be completely in charge of everything that happens in human history – even, mysteriously, evil things, and at the same time react to the prayers of his people and make decisions based upon what we ask him. But the God of the Bible is big enough to do what we humans can’t comprehend. And in fact, this type of God is the God we all need and want: a God who is completely in control of all things and strong enough to fix everything, but also a God who relates to me where I’m at and takes my thoughts and feelings and desires seriously.