You lose a shop either way, that's how the quests are built. And, no, the Junkyard doesn't fully recover - the old Scrappers territory stays abandoned. On the bright side, neither of the stores are really high-end stuff, so once you've finished the Depot A questline and the world opens up, you don't have much cause to go back to those early-game stores. The only merchant in Junkyard that is really end-game viable is Fixer.