1) calibre has an "In Library" column in Device view, which works similarly to the "On Device" column from the Library view.
search:
Do note that in both views, calibre needs the metadata to be the same in order to make a match.
2) Are those books KFX? If so, you might need to upgrade to a newer version of calibre.
EDIT: Because calibre doesn't support KFX (it hasn't been reverse-engineered so we don't know how to convert it). But at least calibre tells you it's there and how to get a "real" copy.
3) No, you cannot send just the metadata. However, as long as the send-to-device
filename template is the same (by default it is based on the title and author) the new copy will overwrite the old copy.
If the filename template is different, then you will need to delete and resend the book, otherwise you end up with two copies.