If a creature is flickered does it come back as a new object and lose its counters?

When a permanent is exiled and returned to the battlefield, it becomes a completely new game object. Under CR 400.7, an object that moves from one zone to another loses all memory of and connection to its previous existence. This means all counters (including +1/+1 or loyalty counters), Auras that were attached, Equipment that was attached, and any other effects that were tracking the 'old' permanent no longer apply.

The returning permanent enters the battlefield fresh, as if it had just been cast for the first time, with only what it naturally has on its card (or what the flicker effect specifies). Auras and Equipment that were attached will also fall off unless they happen to be able to legally re-attach as the creature enters (CR 303.4 for Auras entering the battlefield).

This applies regardless of how fast the flicker happens — even effects that say 'exile it, then return it to the battlefield immediately' create a new object. CR 400.7 is clear that zone changes sever the connection to the previous object.

Concrete example: Your Champion of the Parish has three +1/+1 counters on it. Your opponent flickers it with Cloudshift (exile it, return it to battlefield). It comes back as a 1/1 with no counters — all three counters are gone because the returned creature is a brand-new object.

Note: Some cards specifically say 'return it to the battlefield with counters' or use other phrasing to override this default behavior — always read the card carefully to see if it makes an exception.