This happened during the Thor Event 11/15/2013. I had about 9 standard tokens and a few special tokens stashed. Nefarious and Lightning I believe. After the event was over, I lost all my tokens. Are you supposed to use your tokens before an event is over?
Yes, those tokens were for tournament-specific cover packs. The cover packs go away after the tournament ends.
Ok. What about the Standard Tokens? I earned those through normal gameplay.
If they were normal tokens, they should have remained. Start a support ticket from the gear icon in game and they should be able to look into it.