I once upgraded Y-C between SIN and BKK. And for weeks after that, the Qualiflyer Centre hounded me for my boarding pass and copy of ticket EVEN though it was issued by Swissair themselves and I used miles.
Apparently the system couldnät find me on the flight.. even though on my account it very clearly states that 5000 miles have been deducted for upgrade, PLUS a credit of about 50 Sfr
http://www.flyertalk.com/forum/thumbsup.gifwhen I bought Duty Free onboard!