You should NEVER do anything like that to things in the official Library folders.
Calibre has tools to update the books INSIDE the Library. Pulish and Update Metadata.
Next: Why are you using the O/S (which does not do all the neat, additional Kindle things)?
Metadata Plugboards offer to insert or modify Kindle recognized fields.
Calibre does an outstanding job sending books to a Kindle
I use USB with the plugboard set to insert series_index into the title.
I also use Kindle Collections to turn Series into a 'Collection" (coupled with the plugboard use, series in reading order
)