We have multiple computers and multiple users in our house, so I can't always use the same computer to fix ebook files. And I never copy a fixed ebook file directly back into the Calibre book directory because often the file size has changed (and Calibre doesn't register the change unless I re-import it using the Add Books button). None of this should matter, though, because this method has always worked in the past, and Calibre does have a setting to "overwrite existing book formats," which it is definitely not doing.
Edit: Oops, sorry, I am mixing threads here. Over in Calibre's Library Maintenance section, there is a thread about Duplicate Formats, which is tangentially related to this one. (
https://www.mobileread.com/forums/sho...d.php?t=220948) The problem of orphaned ebooks in Calibre 1.0 is related to the new way of truncating. That problem has now been solved (thanks, Kovid!), which has also solved most of my major headaches with truncation of file names.