In fact, even if you do have an ISBN, we ask that you remove it from the cover file that you upload. When you use the Cover Template Generator on Lightning Source's website, it will require you to enter an ISBN. Simply enter all zeroes (i.e., 000-0-0000-0000-0) for the ISBN. On the cover template you receive, delete the bar code and leave the bar code area a as blank white box on the cover file that you upload to us.
The reason we must ask you to remove your ISBN is a rather complicated matter relating to how our printer, Lightning Source, indexes titles in their database; boiled down to its simplest form, the explanation is that, unfortunately, the software code that passes data back and forth from their server to ours simply does not accept any ISBN.