Hi stachy,
Welcome to our community! 
When you implement the CinemachineBrain to your game, the CinemachineBrain controls your camera. For this reason, it is the expected behaviour that the camera does not ‘work’ anymore. The CinemachineBrain applies the values from the CinemachineVirtualCamera to the Camera component.
If the cinemachine camera ‘follows’ or ‘looks at’ a game object, you also lose control. This is also the correct behaviour.
If a game object suddenly disappears in front of your camera, check which game object the camera follows. If a game object consists of children, and the children get moved, the camera does not follow the children as it cannot split itself up. It follows only the game object assigned to the ‘Follow’ field.
Without knowing basically anything about your project, I’m afraid this is all what I can suggest (for now). I hope it’ll help anyway.
See also:
- Forum User Guides : How to apply code formatting within your post
- Forum User Guides : How to mark a topic as solved