Last night, my partner and I booked the following itinerary on United:

EWR-ZRH on UA (K class)
ZRH-IST on LX (K class)

return trip:
CTA-MUC on LH (W class)
MUC-EWR on UA (K class)

My partner, who is a 1K, was doing the booking with his account.
Prior to payment, the website informed him there was upgrade space available on the MUC-EWR flight, so we selected the upgradable fare class (W) for that segment and were immediately confirmed into BF (R class).

Confirmation email was received from United reflected the above booking and fare classes and price. It had the standard message stated that reservation was not yet ticketed pending confirmation from LX and LH.

When the reservation was finally ticketed and confirmed today, all the flights were now in W class, no upgrade was listed on the MUC-EWR segment and the final ticketing price listed was $818 more than the original purchase price reflected in the initial email.

My partner hasn't yet had a chance to call about this, and I guess we could always just cancel the itinerary, but anyone ever had anything like this happen before and would an agent be able to restore the original itinerary and pricing?