Is draining a Li-Ion to 2.5v harmful to the battery?
Yes, lithium batteries undergo unwanted chemical reactions when discharged below 3V, causing their internal resistance to be permanently and significantly raised. Their capacity will suffer as well, meaning that they won't accept the same amount of charge anymore. When such an overdischarged cell is "brought back to life", it will likely become chemically unstable, creating a risk of a short circuit developing inside the cell.  

Even worse, assuming that you measured 2.5V at no load, your batteries have dropped even lower when they were being discharged and have subsequently rebounded to 2.5 V after the load was removed.  

Li-ion cells have a maximum voltage of 4.2 V or less, I am not sure where you got the 4.7 V figure from but it's a recipe for fireworks. OP has since edited the question, to a still incorrect 3.7 V. 3.7 V is the nominal voltage (average voltage during a complete constant current discharge), while 4.2 V is the maximum voltage. These figures will vary slightly from cell to cell.

I would completely discharge the cells and get rid of them, 2Ah 18650s are cheap and not worth the risk of them blowing up.