[pghaworth]

This happened to me as well, last night. I am running Vista Home Premium 64. Deleted a book file/format because the conversion was bad and I wanted to try again with a fresh, fixed rtf and I wanted both formats to compare results. First I copied the original mobi file and pasted it elsewhere renamed. Then I deleted the mobi file properly from Calibre, saw it was in fact gone, and added the rtf that had been fixed as a book. When I went to merge the mobi file was back in the original place in the library and also in the actual folder.

Please note, that after I deleted the mobil format I had completely closed Calibre, because it seemed to be hanging, and opened it again to add the rtf file.