Pdf files are just like any other files. Therefore, any name change is made the same way as on any other files. I am not sure whether you plan to have two files with the same names in the same folder (question is unclear), but that is not possible.
There are other files that contain other content besides the two .html files. So no, there is no way possible to have two files with the same name on different folders. There were some problems with the .html files that the plugin does not handle correctly, and I've had them fixed on the .zip version that you also are hosting. That version now can be downloaded and installed by the user. However, this is not an option on other sites on which the plugin is hosted. The plugin does not support uploading, as it is impossible to determine to which file each .txt file is attached. That means they cannot both fit in the same .zip file. I'd like to know about the way this plugin works if a .html file is attached. Is there a .php file that is responsible for adding the .html extension to the.