Don't despair.
When I was preparing for my G8 flute, I could happily play for 2 or 3 hours at a time (if I paced myself, and played some pieces that didn't require much effort).
Now (I'm very out of practise) I can manage about 15 minutes before I start feeling tired (so, just as I've got my flute warmed up, I'm too tired to make the most of it!) and another 30 mins after that of things sliding rapidly downhill. I do try and do that extra 30 mins of sounding dreadful though, because after a couple of weeks my tone comes back (ish) and I can play for significantly longer.
And then I lapse for another month or so.
Given time and practise stamina does improve. Doing two or three shorter sessions is a great way to increase practise time and progress, but don't forget to also push yourself to play a little longer (for so long as the ears in the vicinity can bear it, anyway) so that stamina improves as well.