Look what the OP wrote (in a badly formatted way) is

Output from my code 
FILE=fileA
err=99
script:foo.pm
foo.pm
FILE_READ=fileB
err=99
err=20
testset:test1 

Output required
FILE=fileA
err=99
script:foo.pm
foo.pm
FILE_READ=fileB
err=20
testset:test1
[download]

I have the biggest problems seeing a code who could possibly produce err=99 and err=20 out of a hash.

He never gave us the full picture, we had no possibility to know what his real problem is and "what didn't work as expected."

And for completeness the "solution" he posted is IMHO still buggy, b/c it'll filter ALL duplicates, not only for key 'err'.