You probably have some tools or something which add, remove or touch a file in your rom folder. Before fixing roms, romcenter checks all roms folder to see if files are always here.
This is mainly for security reasons. RomCenter can delete a rom if it knows it exist elsewhere on your disk. If you deleted the copy manually and romcenter does not check, it could delete the only remaining files.
Also, note that when a refresh is asked, you have to re-do the task because selection is lost during the process.