"<number> per game" abilities are tracked sort of as a game rule. It doesn't matter how many copies of the card are in your deck, or if you reset any of them to face value, you can still only use the ability the specified number of times total.
Jephthah, whether reset or if you have a second copy, can only activate his ability once per game.
Cards that simply say "limit 2 uses" or "may be used twice" I think are what you're thinking of. Those track uses on a card-specific basis and CAN be reset if the card is shuffled/returned to hand/reset. You can also use it that many times per copy of the card.