"Oh well" is an interjection used to express acquiescence or resignation towards an undesirable event which has occurred (maybe this isn't the most precise definition, but I think most native English speakers know what it means.).
What is the history of this phrase?
A remark: it would sound more logical for it to be "all well" rather than "oh well", because the former would reaffirm that all is still well in spite of whatever bad has occurred.
Alone, "well" has been used as a discourse marker for all of English history. However, "oh well" doesn't seem to be as old. The oldest citation for "oh well" in OED is 1582:
O well quoth Samson, if yee had not plowed with my heyfer, that is, vsed the helpe of my wife, yee had not founde out my redell.
T. Bentley Seuenth Lampe Virginitie in Sixt Lampe Virginitie 299
It is also relevant to note that the nearly identical expression "ah well" is likely older, as the earliest OED citation is from 1534:
Hem, numnam perijmus? Ah wel, are we not in yl case trowe we?
N. Udall Floures for Latine Spekynge gathered oute of Terence f. 16
I always heard it resonate in England as
Oh well if that is the case.
Oh well it could have been far worse.
Oh well I did not know that.
Oh well you came to the right place.
If you where to use well to mean
All is well
Than it simply does not fit into how or why we use this phrase.
It is used as more a way of saying that you understand events and you have accepted them. Usually after someone else has enlightened you to the new course of events.
The 'Well' is more like in these phrases.
Well I will see to it straight away.
Well I won't be going home soon.
Well who knows what the right answer would have been.
I don't know allot about the history, but I think this is somewhat of an emotional expression that is probably older than writing or language itself.
