I just last night upgraded a ticket bought before the new fares were introduced and the mileage cost was at the old rates (I had a W fare, which under the new system is a Flex, not Flex Plus and so on the sector I was upgrading the new cost is 60% more) - so they definitely have the capacity to do it automatically. Mileage earning is also showing the old rates.

This is a ticket I bought in February, so after the 31 Jan cut-off, but under the old fare regime.