$filename = '/path/to/config/file';
open(CONF,"<$filename");
while(<CONF>){
  chomp;
  my ($q, $w) = split(/\t/,$_,2);
  $config{$q} = $w;
}
close(CONF);
$config{'variable'} = 'new contents';

open(CONF, ">$filename");
print CONF "$_\t$config{$_}\n" for keys %config;
close(CONF);