So Fallout 3 wasn't the only one getting update years after being left as it was, Rise and Shadow of the Tomb Raider (also the 2013 Tomb Raider) are getting an update to remove denuvo from it which seems to broke both Rise and Shadow's mods.
Rise of the Tomb Raider has it's own mod Injector which no longer seems to work, Shadow relys on SpecialK tool to inject textures but now the game is pure black when you enter the game.
Anyone else having the same problem? More import
Can confirm ROTTR update revert make my mods work again, this version is build813.
However SOTTR did not get the update revert, to make your mods work again, go to Steam and right click SOTTR in library, select properties - betas, then choose build298, the mods should be working again.