I would just do a one-liner ..

alex@foo:~/tmp$ cat >data.in
443..29D  test.avi
563..D93  xyz
AB2..FFE  a.file
alex@foo:~/tmp$ perl -e 'while(<>){chomp;($md5,$file)=split;$data{$fil
+e}=$md5;}foreach(sort keys %data){print"$data{$_} $_\n";}' <data.in
AB2..FFE a.file
443..29D test.avi
563..D93 xyz
[download]

.. and re-direct to an output file as necessary.