I also think this is what happened, however if you are ATC(or FAA or whatever authority) you simply don't allow planes to fly over a warzone, it's stupid and sooner or later has to result with this...
I fly SIA Heathrow-Changi a couple of times a year and the route takes you straight over the top of Afghansitan and has done since the Afghan business started. It's always been a bit of a bum clencher for me. It also flies very close to the Crimea. I'm off again in a couple of weeks, oh joy. There's a bloody great big NOTAM out in the FIR bit about avoiding Ukraine airspace as well.