Will accidentally leaving an upstairs window open a day or two with central air unit running harm the unit?

It should NOT if your unit has been properly maintained, but your cooling bill may be the biggest issue in the short term. Never hurts to have your unit checked though at least once a year just as a GREAT practice.

I wired one of my customers AC so if any Doors(could add windows, But they NEVER open) were open more that 5 Minutes it will shut off AC, so they are not Air Conditioning the Outside. Also, if Heat or Smoke is Detected, it will shut off AC so it will not Pump Smoke throughout the House, or More Oxygen to the Fire. Used an Alarm Panel, and had Output Follow those Zones. I added a Delay On timer so if AC was JUST turned off, it will not be fighting the Head Pressure. Good Luck