Maybe not an exact situation, but a similar experience:

I often buy my return tickets for my JFK-CDG trips in Premium Economy with the plan of using miles to upgrade to Business Class, with the outbound leg in 'A' and the return in 'W'. The priority is to upgrade the return flight (day flight, longer) while I can survive the short red-eye outbound.

The 'W' full fare on the return makes it easier to upgrade since it taps into not only the 'O' fares, but also the 'Z' fares when you are Elite, and for 22,500 miles. Most of the times, including this one, the agent on the Plat line took care of issuing the initial "A+W" ticket, but process the upgrade at the sale time, into a "A+Z" ticket.

One month later, after monitoring, I get news that an upgrade/award 'Z' fare gets available on my outbound leg (but no 'O'). Therefore, I call the Plat line in order to pay the fare difference between the 'A' and the 'W' and then use my miles.

Common sense is that I would pay only ~350€ (like I did in the past). However, the agent priced it to me for the pretty amount of... 2,700€!!!!! It goes without speaking that I politely declined. I hung up without inquiring why such an expensive price, as I was still under the shock and unnerved by the price.

I however tried again the following day and spoke with another Plat Line agent and explained to her my shock. She looked again and told me the re-pricing would be... 325€!!!!

She explained to me that the previous agent did brainlessly a repricing by following what's on the computer, and what she priced me was the upgrade from "A+Z" into "W+Z". She should have re-priced the original ticket, i.e. calculate the fare difference between a "A+W" into a "W+W".

Because my return fare was fully flexible and fully refundable, the difference impact would be only on the outbound leg. Not sure whether this helps the OP because this implicitly confirms that the whole trip is re-priced.

As for the conclusion of my story, she charged me only the difference she calculated manually and because it was a manual pricing adjustment, she would need to document it, otherwise the Pricing Dept. would make her troubles. I told her I didn't want to cause her any troubles, and she said to not worry, because she documented everything, and if the Pricing Dept. would challenge her, she would have no issue explaining the reasoning.

She also said that she has been working for 30 years, but that a less experienced agent might have not detected the issue with the computer re-pricing methodology. Of course, she processed the upgrade on the outbound leg with miles and I was confirmed with a "Z+Z" ticket.

That lady was so nice and helpful. The conclusion is that even on the P'lat Line, there is inconsistency among the agents in terms of knowledge.

-Vinnyc