If the files are on your Reader, you'll be able to move them back to Connect. Or you can copy them 'out' either by putting them on a memory card or going to the location on disk where they're stored (the names are ugly but they're the same files).
The path should look something like this:
C:\Documents and Settings\[UserName]\Local Settings\Application Data\Sony Corporation\CONNECT Reader\Database\kLibrary
Once you do the de/reinstall, you can put them back. Or you can redownload them from the Connect Store, thought that'd be my last choice, personally.
