There's only one way to change the name of the book file: change the title of the book in the Calibre Library.
If it's really a major issue for you, you could set up a custom field to store the "real" title and then use a modified unique title in the actual Title field.
I don't recommend this unless you're willing to put up with a lot of other limitations. One of the biggest issues is if you're going to be exporting the books to devices that index the metadata title instead of the file name. A metadata plugboard might help here, although I don't use them myself so I don't know for sure.
Also, what program are you using to read these books? Maybe you could find an alternative. I know, it's a lot to ask. People don't like to change their favorite software. But if the current limitations are too much, something has to change in your work flow.
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