I have been trying to put the vanilla resources back into BSA format because I have a bunch of mods that use BSA files, and I believe they won't actually be used in favour of the original resources if the original resources are loose files? Just as a brief example, a number of STEP mods use BSA files; Acquisitive Soul Gems, Convenient Horses, Enhanced Blood, the Paarthurnax Dilemma, the unofficial patches, etc.
However, I've run into a problem in that while the Skyrim - Textures.bsa file went back fine, as did the first HRDLC file, the HighResTexturePack02.bsa resource folder is giving me a "cannot read BSA file!" error at the end when I try to process it back into a BSA file. Does anyone know of anything I could try to make this work, or whether there's a way to have them as loose files without interfering with my mods?