There is an option somewhere in CC's settings to do resync changed books, I believe. Dunno exactly where -- I do my reading on my KT so I don't use chaley's app.
Metadata is stored in CC's database. That is all that CC looks at.
Changing the ebook itself is unnecessary unless you want the reader app to see the changes. But you should be doing any library searching from CC.
I don't know if the resync option is for edited books only or even metadata changes.