I mentioned
k2pdfopt in another thread. It exists solely to convert PDF layouts, so yes, such software does exist. That software even has it's own thread in the PDF forum on this site, so it's not that hard to find. I'm sure it would work fine for converting two column layouts to single column. If all of the papers are of that layout, then all is fine. I've seen many complicated layouts, though, including images and tables and equations that span both columns, and I don't personally know if
k2pdfopt handles those situations well, but there's only one way to find out. Try the software; it's free to use.
Here's the link to the software's site:
http://www.willus.com/k2pdfopt/