Upgrading yellow trinket puts it on cooldown
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When you upgrade your Warding Totem to a Greater Stealth Totem, it gets put on full cooldown, even if it was fully charged when you upgraded it. I would instead expect the new trinket to start with exactly one charge when upgraded, available immediately.
I've never noticed any of the other upgraded trinkets (Greater Vision Totem, Oracle's Lens, Farsight Orb) start on full cooldown.