Part of the purpose of DC publishing Batman Eternal, was to unfuck Nightwing after Geoff Johns outed him.
Spyral had a machine that would erase peoples memories/warp reality and erase all evidence, from Forever Evil onward, that Dick was Nightwing. At the end of the event story, DC used the machine to reset shit for Dick so only the usual suspects knew he was Nightwing.
As for Lex, him knowing Bruce was Batman got dropped like a lot of Geoff's planned JLA stories when DCYou happened. However, IIRC he wasn't affected by the mind wipe machine but Snyder hasn't really done much with it in JLA since then.