How do I reset the persisted object back to initial state?

I have several objects that persist in the game. Now, the problem is when the player goes for new game the second time, these persisted objects have already been eliminated in the second run.

Is there a way to reset the persisted object back to initial state without having to restarting the app?

See the manual.

https://www.scirra.com/manual/125/system-actions:

Reset persisted objects

Across the entire project, reset all objects using the Persist behavior to their initial state (as if the layout has not been visited yet). This is useful when restarting a new game from the beginning again.