backup, backup, backup
I would assume it will but I won't exclude accidents so better be safe than sorry. I know from experience that depending on the type/version you have installed, assumption can be the mother of all f'ups
e.g. there was a PortableApps version once and if uninstalling that one it would kill the whole Calibre folder, including global settings and if your library happened to be located below the same top folder, you'd also lose your books and library specific settings.
So again, backup, backup, backup