Borderlands 3 is only the latest in quite a long line of games getting taken off EGS entirely due to publishers not being fans of Epic's business in this particular case, with Vampire: The Masquerade - Bloodlines 2 having also been removed without much in the way of explanation.
Borderlands 3 removed from Epic Games Store
Though Epic and the publishers will still provide those who've purchased either Bloodlines 2 or Borderlands 3 with discounted copies, it remains quite interesting to see so many publishers trying to evade the Epic Games Store Mega Sale by as wide a margin as possible. Far from elegant, this solution is still arguably more political than outright increasing prices in response to the sale, like Supergiant did with Hades.
2K, the publisher of Borderlands 3, didn't share much either: "We are working closely with Epic and have temporarily removed Borderlands 3 from their storefront. We look forward to the game being back on the Epic Games Store very soon."
Since none of the parties seem interested in sharing what additional information they must be privy to, we can only theorise on what's happening behind closed curtains, now that a number of games and publishers have forcefully opted out of it. Klei, too, decided to try and skip the EGS sale, with Oxygen Not Included temporarily removed from the store as well.