Am I right when I say that these ammended extensions are like aliases?
No, you can replace the original extension using batch rename command and use the plus signs and options in the fields. As long as you are sure the files are original PDF you can safely rename them with '.pdf' and delete the .jpg. But you can't change the files extension itself by renaming as you already have experienced your self, for that you have to use a save as command and choose the extension needed.
And this is also a warning for you to be sure in having proper back up and don't hit to fast OK in batch renaming but look at the preview for the name first