Starting with version 0.85 (Early 2007), BitComet added an option to its torrent maker that ensures that no two data files in a multi-file torrent occupy the same BitTorrent "piece." This helps enable BitComet to download different parts of a multi-file torrent from non-BitTorrent sources such as http/ftp servers or the ED2K network. To accomplish this, BitComet fills the remainder of each last "piece" with an intervening padding file. While these small and harmless files are transparent to the BitComet user, they can be an annoyance to users of other clients who must deal with them both during and after the download. Creation of padding files was enabled by default in version 0.85, and disabled by default in version 0.86 onward
From Wikipedia:
http://en.wikipedia.org/wiki/BitComet
No, unmarking them won't result in the whole download not working properly.