### 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 (!parent_skeleton) {
		PhysicsServer3D::get_singleton()->joint_clear(joint);
		return;
	}
	PhysicalBone3D *body_a = parent_skeleton->get_physical_bone_parent(bone_id);
	if (!body_a) {
		PhysicsServer3D::get_singleton()->joint_clear(joint);
		return;
	}
	Transform3D joint_transf = get_global_transform() * joint_offset;
	Transform3D local_a = body_a->get_global_transform().affine_inverse() * joint_transf;
	local_a.orthonormalize();
	switch (get_joint_type()) {
		case JOINT_TYPE_PIN: {
			PhysicsServer3D::get_singleton()->joint_make_pin(joint, body_a->get_rid(), local_a.origin, get_rid(), joint_offset.origin);
			const PinJointData *pjd(static_cast<const PinJointData *>(joint_data));
			PhysicsServer3D::get_singleton()->pin_joint_set_param(joint, PhysicsServer3D::PIN_JOINT_BIAS, pjd->bias);
			PhysicsServer3D::get_singleton()->pin_joint_set_param(joint, PhysicsServer3D::PIN_JOINT_DAMPING, pjd->damping);
			PhysicsServer3D::get_singleton()->pin_joint_set_param(joint, PhysicsServer3D::PIN_JOINT_IMPULSE_CLAMP, pjd->impulse_clamp);
		} break;
		case JOINT_TYPE_CONE: {
			PhysicsServer3D::get_singleton()->joint_make_cone_twist(joint, body_a->get_rid(), local_a, get_rid(), joint_offset);
			const ConeJointData *cjd(static_cast<const ConeJointData *>(joint_data));
			PhysicsServer3D::get_singleton()->cone_twist_joint_set_param(joint, PhysicsServer3D::CONE_TWIST_JOINT_SWING_SPAN, cjd->swing_span);
			PhysicsServer3D::get_singleton()->cone_twist_joint_set_param(joint, PhysicsServer3D::CONE_TWIST_JOINT_TWIST_SPAN, cjd->twist_span);