$ mkdir zip_root
$ echo "test" > zip_root/test.txt
$ zip -ry test.zip zip_root
	adding: zip_root/ (stored 0%)
  adding: zip_root/test.txt (stored 0%)

$ tree zip_root
zip_root
└── test.txt

0 directories, 1 file

$ unzip test.zip -d test
Archive:  test.zip
   creating: test/zip_root/
 extracting: test/zip_root/test.txt

$ tree test
test
└── zip_root
    └── test.txt

1 directory, 1 file

$ echo "test.1" > zip_root/test.1.txt
$ zip -ry test.zip zip_root
updating: zip_root/ (stored 0%)
updating: zip_root/test.txt (stored 0%)
  adding: zip_root/test.1.txt (stored 0%)

$ tree zip_root
zip_root
├── test.1.txt
└── test.txt

0 directories, 2 files

$ rm -rf test
$ unzip test.zip -d test
Archive:  test.zip
   creating: test/zip_root/
 extracting: test/zip_root/test.txt
 extracting: test/zip_root/test.1.txt

$ tree test
test
└── zip_root
    ├── test.1.txt
    └── test.txt

1 directory, 2 files

$ echo "new test" > zip_root/test.txt
$ cat zip_root/test.txt
new test

$ zip -ry test.zip zip_root
updating: zip_root/ (stored 0%)
updating: zip_root/test.txt (stored 0%)
updating: zip_root/test.1.txt (stored 0%)

$ rm -rf test
$ unzip test.zip -d test
Archive:  test.zip
   creating: test/zip_root/
 extracting: test/zip_root/test.txt
 extracting: test/zip_root/test.1.txt

$ cat test/zip_root/test.txt
new test

$ rm zip_root/test.txt
$ zip -ry test.zip zip_root
updating: zip_root/ (stored 0%)
updating: zip_root/test.1.txt (stored 0%)

$ tree zip_root
zip_root
└── test.1.txt

0 directories, 1 file

$ rm -rf test
$ unzip test.zip -d test
Archive:  test.zip
   creating: test/zip_root/
 extracting: test/zip_root/test.txt
 extracting: test/zip_root/test.1.txt

$ tree test
test
└── zip_root
    ├── test.1.txt
    └── test.txt

1 directory, 2 files

$ zip -h2

Extended Help for Zip

See the Zip Manual for more detailed help

Zip stores files in zip archives.  The default action is to add or replace
zipfile entries.

Deletion, File Sync:
  -d        delete files
  Delete archive entries matching internal archive paths in list
    zip archive -d pattern pattern ...
  Can use -t and -tt to select files in archive, but NOT -x or -i, so
    zip archive -d "*" -t 2005-12-27
  deletes all files from archive.zip with date of 27 Dec 2005 and later
  Note the * (escape as "*" on Unix) to select all files in archive

  -FS       file sync
  Similar to update, but files updated if date or size of entry does not
  match file on OS.  Also deletes entry from archive if no matching file
  on OS.
    zip archive_to_update -FS -r dir_used_before
  Result generally same as creating new archive, but unchanged entries
  are copied instead of being read and compressed so can be faster.
      WARNING:  -FS deletes entries so make backup copy of archive first

$ zip -ry -FS test.zip zip_root
deleting: zip_root/test.txt

$ rm -rf test
$ unzip test.zip -d test
Archive:  test.zip
   creating: test/zip_root/
 extracting: test/zip_root/test.1.txt

$ tree test
test
└── zip_root
    └── test.1.txt

1 directory, 1 file