The most common and most likely answer to this crossword clue is the 1 plus 8 plus 2 plus 8 letter word A BLESSING IN DISGUISE
I've seen this crossword clue in Financial Times
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More clues leading to the result A BLESSING IN DISGUISE
Buddy explains!
The straight part
We know that "an apparent misfortune that turned out well in the end" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case an apparent misfortune that turned out well in the end = a blessing in disguise.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.