I've been wondering a seemingly stupid question, can Supernatural Stamina work more than once on a commander card? Instant grants ability to creature, commander is the same creature while changing zones. Could it be a loophole or am I missing something?
You can not use Supernatural Stamina to return your Commander to the battlefield multiple times.
Whenever a creature leaves the battlefield and returns it is treated as different object. This is covered in the gatherer rulings for Supernatural Stamina:
Supernatural Stamina’s effect works only once. If the targeted creature dies and is then returned to the battlefield, it’s considered to be a new creature. If that new creature dies, it won’t come back a second time.
Additionally, while your Commander is still considered your Commander while changing zones it is still treated as a new object every time it changes zones as covered in the comprehensive rules:
903.3.: Each deck has a legendary creature card designated as its commander. This designation is not a characteristic of the object represented by the card; rather, it is an attribute of the card itself. The card retains this designation even when it changes zones.
400.7.: An object that moves from one zone to another becomes a new object with no memory of, or relation to, its previous existence. There are nine exceptions to this rule:*
*(None of the exceptions apply)
Supernatural Stanima will only protect a creature once; there is nothing different or special about a Commander here.
If you want to use Supernatural Stamina on your commander, then when it is killed; you must choose not to send it to the command zone instead of to the graveyard. If you choose to send it to the command zone, then it will never die, so Supernatural Stanima would do nothing. If you choose not to send it to the command zone, then it will return like any other creature would; but no longer be protected.
From the glossary in the rules:
A creature “dies” if it is put into a graveyard from the battlefield.
So a commander that goes to your command zone won't have died.