You cannot overwrite a file in ROM. Some programs like Resco Explorer or Total Commander appear to let you do it, but the original file is still intact. You can think of it as if the new file is laid on top of the original. Remove the new one and the old one is still there underneath. Replacing the file in a kitchen before you build the ROM is the only way you would lose it entirely.
Just try deleting the old one (with TF3D disabled, of course). The stock Sprint file is attached just for peace of mind
