[BetterRed]

As a general rule don't copy files directly from the library. File names within a calibre library are computed via an algorithm -- the title and author name are latin-ised, and ascii-ised, (e.g 'Война и миръ by Лев Николаевич Толстой' becomes 'Liev Nikolaievich Tolstoi - Voina i mir') and the resultant file names can be shortened as you've see with 'The Hidden Harbor Mystery (Book'. And to cap it all off the algorithm is subject to change.

Exactly where are the notes you need to preserve, and where/how do you create/maintain them - within the library or on your device, as separate files or embedded in the ebook files - or ... or all of the above.

BR