Upgrading the upgrade is not what the function was written to do, so it does not do that. It would require some fundamental code changes to that function to make it do that. This would be a good thing to fix though.
I have a simple policy: Never upgrade facilities to an intermediate level. Like Wanderer I try to research higher levels in quick succesion so as to not be stuck at level 1 for long. I will build level 2 space yards but I will not upgrade to them. Situations can cause me to shelve this policy but that is my rule of thumb.
I use the same policy in upgrading pop transports etc.
But I really find it no trouble to go through my space yarded colonies and delete "Upgrade to SY 2" if I have to. Its only annoying if you have hit the upgrade button by mistake.
Kim
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Those who can, do.
Those who can't, teach.
Those who can't teach, slag.