Instead of forcing players to buy the game yet again, the console versions of Skullgirls Encore will be available for free to anyone who currently owns Skullgirls. The Steam version of the game is unaffected by Konami's IP wrangling, and will remain largely unaffected.
The biggest (and arguably only) addition to Skullgirls Encore is the DLC "Squigly" character. As a mea culpa to the community for having to put up with all of this hassle, Squigly will be available as a free addition to the game for a period of three months, regardless of which console you're using to play the fighter. Unfortunately, the DLC character color packs so far released for Skullgirls are not compatible with the new version, but developer Lab Zero Games doesn't want to have to charge people twice for simple palette swaps and is instead rolling each character's color scheme options into one big polychromatic DLC offering which is also going to be available to players totally gratis.
Full details on the change can be found on Lab Zero's website, just don't go in hoping for reams of Steam changes. The lack of Konami involvement in that version of the game means it's merely receiving a new Skullgirls Encore title screen.