Near the end of the event, it seemed that some aircraft ordinance was reset to 0, but can't say if all or only some aircraft were affected. But I too first noticed that my il-40p wasn't loaded up about a minute into the game and I'm asking myself...did I use them already? In hangar they were set to 0 somehow. Someone else at that time had similar issue in clan chat.
From what I can gather, it doesn't seem to be a persistent issue after the first time it has occurred and you've resupplied your ordinance. Definitely something to keep in mind when the next event occurs.
Thanks for the report!