Bach FAQ 59
Yes and no. You have to check my answer precisely.
No, the whole work never has been missing, like you read it often. However, some eighty years after Bach's death nobody in the public was interested in Bach's music. Nobody wanted to listen to it and nobody wanted to perform it. That didn't change until German Composer Felix Mendelssohn Bartholdy, who adored Bach reperformed the St. Matthew Passion for the first time, 101 years after it's debut performance. In general this is meant, when you hear that Bach's complete work was missing for almost hundred years.
On the other hand, you can relate the question to some 10, 000 works, which are missing according to Professor Christoph Wolff, Bach expert and Bach author. He assumes this number of works had once been created by Johann Sebastian Bach. Out of these more than 11,000 works today there are 1,128, a few more or less ( ... considering the past and the future), preserved. Viewed from this angle almost the whole work of that exceptional composer would indeed be missing, destroyed - just gone. Which is, as mentioned reduced by the ten percent which we still enjoy with much excitement today.
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