Not sure if I totally understand, but I'd like to help if I can! So you have an archived version of your index.html but it isn't exactly the same as what you had before? Is "single file" an archival tool? By nature those are likely to take all of the dependent files (images, CSS) from your page and smash them together, so the issues you're seeing are probably related to that.
It'd help if you post the complete source code for your archived index.html, and then maybe describe what's wrong in bullet points so we can help sort it out. :)