Does a creature that phases out retain counters and attached auras when it phases back in?

When a permanent phases out, it is treated as though it doesn't exist for most purposes, but it does not physically leave the battlefield in a way that would cause 'leaves the battlefield' or 'enters the battlefield' triggers to occur. Crucially, its physical state — including counters, Auras, and Equipment attached to it — is preserved exactly as it was (CR 702.26b, 702.26e).

Auras, Equipment, and Fortifications attached to a phasing creature phase out along with it simultaneously and phase back in with it simultaneously. They are called 'indirect phase-outs' (CR 702.26c). Because they phase out indirectly, they are not treated as separate phase-out events and remain attached to the creature when it returns.

Counters on the phased-out creature also remain on it throughout the phase-out period. Since phasing in does not count as entering the battlefield (CR 702.26e), no 'enters the battlefield' effects reset or interfere with those counters.

Concrete example: You control a Quirion Ranger with three +1/+1 counters on it and a Shimmering Wings Aura enchanting it. It phases out at the beginning of your untap step. On your next untap step, it phases back in still bearing all three counters and still enchanted by Shimmering Wings — nothing is lost or removed.

The only things that change for a phased-out permanent are that it is ignored by the game rules while phased out (it can't be targeted, doesn't affect the board state, etc.). Its intrinsic properties and attachments are fully restored the moment it phases back in, with no 'enters the battlefield' trigger fired (CR 702.26b, 702.26e).