### 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)

JointData::_get_property_list(p_list);
	p_list->push_back(PropertyInfo(Variant::FLOAT, PNAME("joint_constraints/bias"), PROPERTY_HINT_RANGE, "0.01,0.99,0.01"));
	p_list->push_back(PropertyInfo(Variant::FLOAT, PNAME("joint_constraints/damping"), PROPERTY_HINT_RANGE, "0.01,8.0,0.01"));
	p_list->push_back(PropertyInfo(Variant::FLOAT, PNAME("joint_constraints/impulse_clamp"), PROPERTY_HINT_RANGE, "0.0,64.0,0.01"));
}
bool PhysicalBone3D::ConeJointData::_set(const StringName &p_name, const Variant &p_value, RID j) {
	if (JointData::_set(p_name, p_value, j)) {
		return true;
	}
	bool is_valid_cone = j.is_valid() && PhysicsServer3D::get_singleton()->joint_get_type(j) == PhysicsServer3D::JOINT_TYPE_CONE_TWIST;
	if ("joint_constraints/swing_span" == p_name) {
		swing_span = Math::deg_to_rad(real_t(p_value));
		if (is_valid_cone) {
			PhysicsServer3D::get_singleton()->cone_twist_joint_set_param(j, PhysicsServer3D::CONE_TWIST_JOINT_SWING_SPAN, swing_span);
		}
	} else if ("joint_constraints/twist_span" == p_name) {
		twist_span = Math::deg_to_rad(real_t(p_value));
		if (is_valid_cone) {
			PhysicsServer3D::get_singleton()->cone_twist_joint_set_param(j, PhysicsServer3D::CONE_TWIST_JOINT_TWIST_SPAN, twist_span);
		}
	} else if ("joint_constraints/bias" == p_name) {
		bias = p_value;
		if (is_valid_cone) {
			PhysicsServer3D::get_singleton()->cone_twist_joint_set_param(j, PhysicsServer3D::CONE_TWIST_JOINT_BIAS, bias);
		}
	} else if ("joint_constraints/softness" == p_name) {
		softness = p_value;
		if (is_valid_cone) {
			PhysicsServer3D::get_singleton()->cone_twist_joint_set_param(j, PhysicsServer3D::CONE_TWIST_JOINT_SOFTNESS, softness);
		}