I have today had this problem happen to me as well. 8 hours into my 12 hour flight my client crashed "Error- application must close etc". I suspect my connection to my wireless internet might have dropped as PlutonainEmpire suggested.
So, despite my aircraft still cruising smoothly enroute right now (about three hours to go) I guess this flight is lost? I had to close the client so I guess any chance of a manual upload is ot of the question.
I'll forward along a failure log if I can find it as mentioned here, and will try and figure out someway to get out of my booking without losing any money
Edit: (a few hours later) I've sent my logout to Konny at the email address listed above. Thanks!

I've also reworked my home network and my flightsim computer is now hardwired to the internet, instead of through a wireless connection. That might solve my problem.