There was a dev post earlier today shared by Damix on Discord that addressed the T6 token issue. Don’t worry, you won’t have lost any of your progress. No need to do anything on your part currently. When the last TFO event ended, it seems that they may have accidentally removed the progress display. So the 2 things are related. Right now, there isn’t an event happening that you can earn more tokens (that I am aware of anyway), but they will probably have something when the new content goes live on Tuesday.
A special TFO event will recur at (semi) regular intervals, so even if for whatever reason you may miss one there’s another on the horizon. According to the Devs with regular gameplay (which includes missing/skipping an event) you will still be able to earn enough tokens to get your T6 ship around August.
The next special TFO event will most probably be a ground one.