In the blink of an eye, he was/had gone

The meanings are similar: In the blink of an eye/a very short period of time:

Using verb 'to go':
he had gone = he had departed or left.

Using verb 'to be gone':
he was gone = he was not there any more, or had vanished.

In Canada, 'was gone' often means that someone has died.

In the first sentence, it would suggest that someone had died quickly/unexpectedly.

Good'n Beth, not oft somebody aces Cen

As Ehbeth says "to be gone" has two main meanings:

a) to be no longer in a particular place
The door slammed and he was gone.
I turned round for my bag and it was gone.

b) to be dead or to no longer exist
His wife’s been gone for several years.
Many of the old houses are gone now.

He had gone: focus of attention on his going.
He was gone: focus of attention on the fact that he was no longer there.

A modern example in the movie "Nightfall", 87th minute from the start:

Ex-MI6 agent Silva (Xavier Bardem) manages to escape from the glass cage where he'd been confined and kills a couple of guards for good measure.
James Bond (Michael Craig) arrives on the scene of the killing and sees that Silva has disappeared.

James Bond: "He is gone!".

Tnx Cen, knew u'd come thru !!