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Have you removed every one of those and confirmed they are shorted? Because if you are only testing them on the board, and all of them are in parallel on there, then odds are only 1 of them is actually shorted.
If the short at C6/C7 is still there then I'd suspect U1 is bad, since C6/C7 are on the 5v rail, which is the input of U1, then pretty much every other cap you checked are on the output of it. U1 is an MP2161, but I'd pull it and make sure the shorts go away first.