### 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 (simulate_physics == p_simulate) {
		return;
	}
	simulate_physics = p_simulate;
	reset_physics_simulation_state();
}
bool PhysicalBone3D::get_simulate_physics() {
	return simulate_physics;
}
bool PhysicalBone3D::is_simulating_physics() {
	return _internal_simulate_physics;
}
void PhysicalBone3D::set_bone_name(const String &p_name) {
	bone_name = p_name;
	bone_id = -1;
	update_bone_id();
	reset_to_rest_position();
}
const String &PhysicalBone3D::get_bone_name() const {
	return bone_name;
}
void PhysicalBone3D::set_mass(real_t p_mass) {
	ERR_FAIL_COND(p_mass <= 0);
	mass = p_mass;
	PhysicsServer3D::get_singleton()->body_set_param(get_rid(), PhysicsServer3D::BODY_PARAM_MASS, mass);
}
real_t PhysicalBone3D::get_mass() const {
	return mass;
}
void PhysicalBone3D::set_friction(real_t p_friction) {