### 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)

angular_damp_mode = p_mode;
	PhysicsServer3D::get_singleton()->body_set_param(get_rid(), PhysicsServer3D::BODY_PARAM_ANGULAR_DAMP_MODE, angular_damp_mode);
}
PhysicalBone3D::DampMode PhysicalBone3D::get_angular_damp_mode() const {
	return angular_damp_mode;
}
void PhysicalBone3D::set_linear_damp(real_t p_linear_damp) {
	ERR_FAIL_COND(p_linear_damp < 0);
	linear_damp = p_linear_damp;
	PhysicsServer3D::get_singleton()->body_set_param(get_rid(), PhysicsServer3D::BODY_PARAM_LINEAR_DAMP, linear_damp);
}
real_t PhysicalBone3D::get_linear_damp() const {
	return linear_damp;
}
void PhysicalBone3D::set_angular_damp(real_t p_angular_damp) {
	ERR_FAIL_COND(p_angular_damp < 0);
	angular_damp = p_angular_damp;
	PhysicsServer3D::get_singleton()->body_set_param(get_rid(), PhysicsServer3D::BODY_PARAM_ANGULAR_DAMP, angular_damp);
}
real_t PhysicalBone3D::get_angular_damp() const {
	return angular_damp;
}
void PhysicalBone3D::set_can_sleep(bool p_active) {
	can_sleep = p_active;
	PhysicsServer3D::get_singleton()->body_set_state(get_rid(), PhysicsServer3D::BODY_STATE_CAN_SLEEP, p_active);
}
bool PhysicalBone3D::is_able_to_sleep() const {
	return can_sleep;
}
PhysicalBone3D::PhysicalBone3D() :