Yes! You can continue to add files to your record on the Internet Archive. You can also create a new record for another season of your show, if the number of files in one record is getting unwieldy. I say "record" to refer to the page that looks like this which contains all the descriptive information about the show, and can include many files.
Nope, you're good. The file has already been compressed in a lossy way, meaning that some of the data is gone. We can't get it back. If your files are in a lossy compression format, you only need to change it if that format is obscure or proprietary. We can't get into encoding stuff (the scope! it creeps!) so it's enough to say that your mp3 is probably stable longterm if we get it in the Internet Archive.
Honestly, I'd encourage you to instead add a disclaimer to the description saying that whatever happened no longer reflects you values. I think growth is important, and erasing our mistakes doesn't help the historical record.