I was in this situation over the prior gratuity increase. Prepaid at the lower rate. Onboard, the current higher rate was charged daily, with a corresponding credit of the (slightly lower) daily amount I'd prepaid. Brought up the discrepancy, and was offered to complete the 'usual' form to request lowering of the gratuity. Not a big deal, but it did leave a bad taste. I believe most lines honor the prepaid amounts (for....everything!) or else what's the point?