Check your actual guild conquest tab. If it says that you failed.. when you are certain you won... then yea, it's a problem.
In my case.. we were about 100k ahead of 10th place when I logged with 4 hours to go. So it's not a guaranteed win. Point was, that with everything being yanked and it saying we failed.. I'd like to actually see proof of that. (Given the fact that the conquest system has been in varying degrees of being broken for a couple months now.)
And the fact that this is the day that they chose to make the switch over, means that I'm not even certain anyone from bioware is even checking on it... and I know submitting a ticket wouldn't get any sort of response until next week.. and by then it won't even matter.
Problem is, after that fiasco 2 months ago, I've gotten into the habit of taking screenshots once the clock runs down to prove that we in fact did get the place I say we did. Converting to the Answers page, and shutting down the one on the board the same day something like this happened game-wide really ticks me off.