You mean: the union of dest-dir-1 and dest-dir-2 should equal your
source-dir?
Try rsync -a source-dir/ dest-dir-2/ --compare-dest=dest-dir-1/
This one will even dutifully copy those files from source-dir which
can't be found either in dest-dir-1 or in dest-dir-2.
If you only want to /see/ what would be copied (always a good idea
when trying untested advice from random folks on the internets :)
there's the option --dry-run. Perhaps add the option -v.
Rsync is magic.
Cheers
Rsync wasn't helpful in my case. It refused to recognize file names
properly, complaining about charset encoding, not even with --iconv
parameters.