No no, I don't think he is reading till EOF - he is reading some multipart mime type file with a mark, I guess.
But the problem with the Buffered Reader is, it reads buffered. (big surprise

Therefore the underlying InputStreamReader is read wider, than to last 'readLine'-position.
As far as I know, you may not change the horses on the fly, switching from BufferedReader to ZipReader or something.
Closing the file, and rereading should work.