First of all it is not a "Getopt problem". The error message comes from cp ins your system() calls. The logical Problem of $xmllocation and $xsllocation never being empty strings is another.

GetOptions(
   "u|updated:s" => \my $update,
   "x|XMLFile:s" => \my $xmllocation,
   "e|XLSFile:s" => \my $xlsfile,
);
$update or die "...";
$xmllocation or print "blabla";
$xlslocation or print "blablabla";
#And in your routine
system(qq(sjdks $xmlfile)) if $xmlfile;
#dito for $xlsfile
[download]

I prefer the non-global method, in this case it saves variables. Consider using File::Copy for copying your files, it's better.

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