Cloud file services (copy, Dropbox...) fight with Calibre's name changes.
You must pause those (at least on the Library) when using Calibre.
Not limited to the following issues: (there is a FAQ section on this)
You changed a name,
Calibre moved (renamed the folders) the book.
The cloud tried to put (synch) the old folders back
(covers,OPF are usually smaller, so they got done fast)