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no, your lighting bolt is removed from the game and if you somehow get isochron back into play you need to imprint a new card

Here's the technical details.

Isochron Scepter
Imprint — When Isochron Scepter enters the battlefield, you may exile an instant card with converted mana cost 2 or less from your hand.
2, Tap: You may copy the exiled card. If you do, you may cast the copy without paying its mana cost.

The Scepter's first ability exiles the Lightning Bolt. The Bolt will stay exiled indefinitely (sans weird stuff like Pull from Eternity).

The Scepter's second ability refers to "the exiled card." This is an instance of "linked abilities:"

607. Linked Abilities

607.1. An object may have two abilities printed on it such that one of them causes actions to be taken or objects to be affected and the other one directly refers to those actions or objects. If so, these two abilities are linked: the second refers only to actions that were taken or objects that were affected by the first, and not by any other ability.

Great. But what happens if the Scepter leaves the battlefield?

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 exceptions to the rule, listed immediately after it, for some effects that need to track moving objects in order to function, like Rancor's triggered ability, but none of those exceptions apply here)

So if the Scepter leaves the 'field, it "forgets" that it exiled the Lightning Bolt, so its second ability will have no "exiled card" to reference.

Of course, if the Scepter reenters the 'field, its first ability will trigger again, and you'll have an opportunity to imprint something else.