No zip versão 3.0 existe:
The new File Sync option (-FS) is also considered a new mode, though it
is similar to update. This mode synchronizes the archive with the
files on the OS, only replacing files in the archive if the file time
or size of the OS file is different, adding new files, and deleting
entries from the archive where there is no matching file. As this mode
can delete entries from the archive, consider making a backup copy of
the archive.
Acho que é isso que você procura depois?
Se você fizer quiser manter os arquivos no arquivo, então -u
o fará:
$ mkdir test && touch test/{flibble,foobaz,blurp}
$ zip -r test test
adding: test/ (stored 0%)
adding: test/foobaz (stored 0%)
adding: test/flibble (stored 0%)
adding: test/blurp (stored 0%)
$ rm test/flibble && touch test/{,flibble}
$ zip -ru test test
updating: test/ (stored 0%)
updating: test/flibble (stored 0%)
$ unzip -l test
Archive: test.zip
Length Date Time Name
--------- ---------- ----- ----
0 2013-08-15 22:04 test/
0 2013-08-15 22:04 test/foobaz
0 2013-08-15 22:04 test/flibble
0 2013-08-15 22:04 test/blurp
--------- -------
0 4 files