You seem to be opening the output files multiple times in the foreach loop at the end, that will not only affect the running time but also can be the source of your data lost issue. So open the file before looping:

open my $fh, '>>', $filename;
foreach my $uniquekey ( keys %myHash ) {
   ...
   print $fh ...;
};
close($fh);
[download]

If this is a one time script then don't worry *much* about the following but if you have to maintain it over time consider the following:

• use strict and use warnings
• Naming Conventions, variables like myHash, uniquekey, ... complicate understanding the script, instead use name that reflects their contents
• Use proper scope and define variables only when you need them
• Instead of `ls | grep CVS` use opendir, readdir functions
• Use functions to divide the code into meaningful pieces
• Use autodie
• Use three arg open calls instead of sysopen

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