I had the same problem and found a solution in comment No. 38 from William Dennis there http://s3tools.org/s3cmd-sync
If you have:
$s3cmd sync βverbose s3:
Change it to:
$s3cmd sync βverbose s3://mybucket/ myfolder/
Then the MD5 hashes are compared and everything works correctly! -skip-existing works.
To repeat, both -skip-existing and md5-verification will not happen if you use the first command, and both work if you use the second (I made a mistake in my previous message, since I tested 2 different directories).
Alex f
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