If the battery will not hold the same charge, that is something to worry about. When you say it will not hold the same charge, what does that mean? I live in an apartment, that too on the 2nd floor. There is no way of the key being within a few meters of the car all night. I keep my other car key beside the Prius SKS key and so i know that it is no where near the car. Frankly, i am not sure what happened and why the battery got discharged.
SKS will shutoff if it detects the key for more than a set period of time. I don't remember the exact number.. something like 5-15 minutes. Touching the door handle reactivates the system, iirc. This is from my Gen II experience, but I would imagine that the Gen III has a similar protection.
The same thing happened to my car 3 to 4 times .Z solutions is just The same thing happened to my car . It is indication of weak battery (12 vol) . When I jump start it everything gets ok .