### Godot version

Godot 4 stable and Godot 3.x LTS

### System information

Fedora linux

### Issue description

If you use some custom logic inside _integrate_forces() to alter the state linear velocity and there is any reference to linear_velocity in physics process, the result in godot 3.5 is that it moves just a little bit, while in godot 4 is totally still.

### Steps to reproduce

For the example i created a simple scene in which i apply a force on the linear velocity in  _integrate_forces()  and added a line that add zero to it in physics process. You will not see any move, but it will work fine if you comment the line adding zero.


### Minimal reproduction project

[PhysicsBugReproduction.zip](https://github.com/godotengine/godot/files/12139772/PhysicsBugReproduction.zip)

if (collision_state.floor || !p_was_on_floor || p_vel_dir_facing_up) {
		return;
	}
	apply_floor_snap();
}
bool CharacterBody3D::_on_floor_if_snapped(bool p_was_on_floor, bool p_vel_dir_facing_up) {
	if (up_direction == Vector3() || collision_state.floor || !p_was_on_floor || p_vel_dir_facing_up) {
		return false;
	}
	// 
	real_t length = MAX(floor_snap_length, margin);
	PhysicsServer3D::MotionParameters parameters(get_global_transform(), -up_direction * length, margin);
	parameters.max_collisions = 4;
	parameters.recovery_as_collision = true; 
	parameters.collide_separation_ray = true;
	PhysicsServer3D::MotionResult result;
	if (move_and_collide(parameters, result, true, false)) {
		CollisionState result_state;
		// 
		_set_collision_direction(result, result_state, CollisionState());
		return result_state.floor;
	}
	return false;
}
void CharacterBody3D::_set_collision_direction(const PhysicsServer3D::MotionResult &p_result, CollisionState &r_state, CollisionState p_apply_state) {