I've been using Calibre for a while, but I'm still pretty much a noobie. I didn't know about the empty book issue.
My main effort has been to get my entire physical collection catalogued in Calibre, whether I have ebook versions of them or not, since I really like the database management tools and metadata / covers lookups. I started off building that manually, using empty books, but recently realized I could do it much quicker by taking my list from BookCollector and using that to generate a collection of text files. (List in Excel, used excel to generate good old command language echo the author,title, isbn into a text file with the name also having that info) The I used a matching regex to import all those text files into a fresh library, and I'm going through each one to update metadata and cover and drop in the ebook if I have it.
I guess now I'll leave the dummy text file if I don't have an ebook, so I don't have issues copying in the future. I also kind of like that if I add a zipped text file, it stays as "Zip" format, and doesn't overwrite the dummy text file. That little file is a good reference for me to make sure I haven't messed up something when updating metadata.