Is it permissible to deduct previously paid usurious certificate returns as zakat from the total interest that must be returned to charitable causes, and is intention required for that?

The repentant individual should improve their dealings with interest (riba). Interest is tied to the financial liability of the one who earns it, not to the specific asset itself. Any zakat paid on the principal from an interest-bearing account is valid, and the fact that it comes from an interest account does not make the money itself unlawful, because money does not become designated (or unlawful) by mere designation. The amount of unlawful interest must be disposed of and given to the poor or spent on general Muslim welfare.