Logged in on character A (legacy), moved a bunch of keys from inventory to the new Keys tab.
Logged out of character A. Started a new character B in Season.
Logged back into character A (legacy) and all the keys in the Keys tab are gone. 
Edit: Also, the Keys tab has now vanished completely…
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Same happened to me. Fill a in-game bug report like I did. But unfortunately I think there is no much to do about it
Keys still not showing up after the hotfix 1.2.0.1
Edit: Keys TAB also keeps disappearing and reappearing randomly…
Same problem here. Over a hundred keys and several harbinger eyes from cycle are still gone from the key tab even after the 1.2.0.1 hotfix.
That’s no good!
Hopefully EHG will address, given it’s data loss of items which isn’t great at all.
I have the same problem. All my legacy keys are gone. This would be a huge blow to my motivation to play the game. This is the first time in an arpg that I don’t play season, because I just want to continue my progress from last season and frankly am tired of the seasonal model in arpgs. I think it’s great that in LE I don’t miss out on features, when I don’t play the season. I really hope that they can resolve this bug.