Perhaps just go into the app data interface and “See” the file. That will expose its true URL. Then you might see where things are going wrong for you.
(You don’t say how it is that you’re coming up with the file’s url as just being protocol//filename. That would be useful info. This might be one of those “offer to expose your editor” things. The issue you’re having doesn’t relate to Select PDF. It’s about file handling in Bubble.)