I agree with Herman. For what it's worth, it's the approach we take - update countries/regions (and sectors) in our system and IATI files as the project evolves. This can create discrepancies in our data, for instance between what was reported to the DAC at the beginning of the project and what's in our current IATI files 2 or 3 years later, but that comes with the territory - IATI is meant to provide timely, up-to-date data, not a statistical record.
It's an interesting question nevertheless. @SJohns, are the organizations having problems in their reporting because of the changes, ie is anyone actually asking for the changes to be recorded?
I wonder is an easier solution would be to add an attribute to the country/region percentages indicating if they are modified. Data users for whom this is important could seek details from the publisher?