Rigidbody is behaving abnormally when transformed manually

In my game player is a rigidbody. He can control other characters by being inside it. The characters are also rigidbodies.

So for that when capturing a character i am setting player's parent as that character and transforming its position, scale, rotation.

 public function Capture() {
     (player.GetComponent("RigidbodyFPSController") as RigidbodyFPSController).enabled = false;
     (player.GetComponent("MouseLook") as MouseLook).enabled = false;
     playerFlashLightState = playerFlashLight.light.enabled;
     playerFlashLight.light.enabled = false;
     
     player.rigidbody.isKinematic = true;
     Physics.IgnoreCollision(player.collider, collider, true);
     player.rigidbody.Sleep();
     
     player.transform.SetParent(eye.transform, false);
     player.transform.localPosition = Vector3(0, 0, 0);
     player.transform.localEulerAngles = Vector3(0, 0, 0);
     player.transform.localScale = Vector3(0.01, 0.01, 0.01);
     
     rigidbody.isKinematic = false;
     (GetComponent("RigidbodyFPSController") as RigidbodyFPSController).enabled = true;
     (GetComponent("MouseLook") as MouseLook).enabled = true;
     
     ScreenFader.FadeInScreen();
     
     animator.SetBool("Captured", true);
     captured = true;
 }

And when releasing it i am reverting everything again

 public function Release() {
     player.transform.SetParent(null, true);
     player.transform.Translate(0, player.collider.bounds.size.y/2 + collider.bounds.size.y, 0);
     player.transform.eulerAngles = Vector3(0, player.transform.eulerAngles.y, 0);
     player.transform.localScale = Vector3(1, 1, 1);
     
     player.rigidbody.isKinematic = false;
     Physics.IgnoreCollision(player.collider, collider, false);
     player.rigidbody.WakeUp();
     
     (player.GetComponent("RigidbodyFPSController") as RigidbodyFPSController).enabled = true;
     (player.GetComponent("MouseLook") as MouseLook).enabled = true;
     playerFlashLight.light.enabled = playerFlashLightState;
     
     rigidbody.isKinematic = true;
     (GetComponent("RigidbodyFPSController") as RigidbodyFPSController).enabled = false;
     (GetComponent("MouseLook") as MouseLook).enabled = false;
     
     ScreenFader.FadeInScreen();
     
     animator.SetBool("Captured", false);
     captured = false;
 }

Above codes are attached to the controllable characters.

But after this, the player rigidbody starts behaving abnormally. Sometimes it wont collide with anything, sometimes it would just keep jumping without any reason, sometimes applied force sets it to wrong direction. Which happens randomly for different combinations of transforms.

But if I just change some rigidbody parameter from inspector and revert it (e.g. if i check and uncheck useGravity), it starts to behave normally again.

Is there something I need to do like refreshing the ridigbody or something?