Spoilers: it's not that they retconned all of Steve's backstory from the beginning. It's that Red Skull is having some fun with the Cosmic Cube and time travel. But it certainly did shake things up. Well, the "secretly a Hydra agent this whole time" version of Cap is headed to HeroClix in the Avengers/Defenders War set.
From the preview:
We continue our look at the chase figures from the upcoming Marvel HeroClix: Avengers/Defenders War set by visiting a star-spangled Avenger whose origin story has received a much-debated revision thanks to some tinkering from the Red Skull. Make way for Captain America, agent of Hydra!