The cilnarto is overwhelming
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There is really no way to remove an ingredient once added to a mixture. However, the most reliable way to fix it is to make another batch of sofrito - without the cilantro - and then combine the two batches. Use half for your current dish and freeze the other half for a later meal.
Since the onions etal are already sauteed, the freezing won't have any serious effect on the texture.
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