In calibre, a device driver like the wireless device connection is not allowed to change the file path specified by calibre. The "rules" say that calibre is in charge.
If you are using CC's file templates and if the "Replace existing book files" option is checked, it is possible for CC to change the file name for a book, for example if the title changes and the title is part of the file name. This creates a situation where CC break the calibre rule, changing the file name without calibre's permission. The result: calibre thinks the file with the new name is a new book. Until you disconnect you will see both the old and the new book in calibre. If you disconnect and reconnect, the problem goes away. CC and calibre will agree about what is on the device.
We understand that this behavior is confusing. To help with the confusion, we show a pop-up message (a "toast") on the device running CC saying that calibre might show the wrong number of books.
There is no mechanism for us to show a message in calibre.