One last try (sometimes an issue nags):
$ find A -exec md5sum '{}' + > a-md5
$ find B -exec md5sum '{}' + > b-md5
$ cat a-md5 b-md5 > All
$ sort -u -k 1,1 All > dupes

Now, (I hopefully got my head around it this time...), the dupes file
should contain a list of files that exist in _both_ A and B; but every
two files that have the same md5sum will have _only one_ of them
listed (either in A OR B). So if you delete that list of files you
should end up with only unique files in both locations.

-- 
Ahmad Samir
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