What happens if you flicker a commander with a blink effect that exiles and returns it?

When a blink effect exiles a commander, a replacement effect applies: the commander's owner may choose to send it to the command zone instead of exile (CR 903.9a). This is a replacement effect that changes where the commander goes, so it never actually enters exile at all if that choice is made.

If the commander goes to the command zone instead of exile, the blink effect is waiting to return a card from exile — but nothing is there. Because the card never went to exile, most blink effects will fail to find it and return nothing. The commander simply stays in the command zone, where its owner may cast it again for its commander tax (CR 903.8).

However, if the owner chooses to let the commander go to exile (declining the replacement), the blink resolves normally: the commander goes to exile and then returns to the battlefield as the effect specifies. The commander's 'died/exiled' zone-change counter resets, and it returns without any previously attached Auras or Equipment (unless the blink effect specifies otherwise).

Example: You cast Ephemerate targeting your commander Meren of Clan Nel Toth. You may choose to redirect Meren to the command zone. If you do, at the beginning of the next end step, Ephemerate's delayed trigger finds nothing in exile and Meren stays in the command zone. If you let Meren go to exile instead, she returns to the battlefield at end of turn normally.

Note: Some blink effects use a specific exile zone marker (like exiling 'with' or 'under' a card). In those cases, the effect tracks the object — but because the commander replaced exile with the command zone, it still cannot be found in exile by the returning part of the spell (CR 400.7, 903.9a).