This has been my take on it too, at least with Wally. The Wally now isn't the pre-Flashpoint Wally but the New 52 Wally that existed with the other New 52 characters but got erased by Abra Kadabara. Then he gained memories of the pre-Flashpoint Wally through some MacGuffin or excuse and that is where we are now with him mostly. The Titans run made that very clear and went out of their want to explain the difference.