KARFA - thanks for highlighting that thread! (I did my searches but couldn't find it..) - exactly what I was looking for! The issues experienced by carsnoceans in the thread you referred seem to mirror those I mentioned.

So ultimately what I can gather from the information in this thread along with my experience below:

- Additional YQ should only be charged for the upgraded sector if done correctly

- 'The system' used by BA agents to quote 'automatically' (I believe this is called Pegasus - feel free to correct, anyone in the know!) will apply any tax increases for the full fare component (e.g. one whole direction in a return journey) and thus, applies the incorrect YQ tax

- When agents have to 'calculate taxes manually' as appears to often be the case, they will depend on their skills to apply this correctly using their native booking system, Amadeus

Thus - in conclusion - for any partial UUAs with two longhauls (your comment makes sense - it shouldn't be an issue for EU or domestic UK connections) it is an absolute must to be armed with correct applicable tax amounts for example from ITA (thanks Globaliser!) unless you want to pay a higher amount than that due. I am not a fan of having those discussions with any agent - let alone the 'less good ones'..

Appreciate the complexity of fares and tax calculations but it does seem like those designing the Pegasus booking interface (if that is what it is called) has chosen to settle for imperfection on this and accept that they are overcharging.

Yet another reason why UUAs and other changes are so difficult to handle online - and so unlikely to change as BA is happily collecting extra revenue.