To completely uninstall a mod, delete everything in resources except the packed folder, don't touch that one (original untouched game files). And no, uninstalling/reinstalling the game won't help, Steam can't delete modded files. ;-)

Let me guess. You're creating a Afterbirth mod and edited Rebirth texture files? :P
Use Afterbirth versions, located here:
afterbirth.a\resources\gfx\[wherever you want]