Can cherry puree sour if left too long in secondary?

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This is my second attempt to make a quality batch of beer.

I started with an extract brew kit for an 8.1% ABV stout. I added about 4 oz of sweet baker's chocolate, 6 oz of semi-sweet baker's chocolate and about 6 oz of unsweetened organic cocoa powder to the boil. I also added one pound of lactose milk sugar and a "BrewVent" alcohol boost kit supplied by Austin Homebrew Store.


After two weeks in primary, I racked onto 49 oz of Oregon sweet cherry puree and 8 oz of organic Guana cocoa nibs. After about 5 weeks in the secondary better bottle, the krausen has thickened and the beer smells funky. I am afraid the fruit has rotted and will now create a sour cherry stout. This is far removed from what I had initially envisioned when I set out to create what I Christened "Milk Chocolate Covered Cherry Stout."


Additionally, the nibs and cherry puree has remained almost completely at the bottom of the carbory since shortly after racking.


The final step will be to add 2 oz of black cherry extract with the priming sugar at bottling.


As always, thanks for the help. And, if someone can get that Revvy guy to post on my message thread, I would be honored.
 
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