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It's probably an issue with Hero Lab. The spells show up on the Spells or Racial Spells tab and not on the In-Play tab where the Short Rest button is, so I get the feeling it's tab focused for abilities that show up on that tab.
I would see if reporting it as a bug gets any response.
A workaround would be to create a Racial Special and copy/paste the spell information into it and put a tracker on it where it says "Show in Tracked Resources". This would cause the copied "spell" to show up on that tab and force the tracker to reset.
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