Take a look at perldoc perldiag under the explanation for the error message (specifically "Filehandle %s reopened as %s only for input"). You're closing STDOUT, the subsequent open of MYFILE gets the STDOUT filehandle id, and since you're only opening that for reading Perl warns you about this seemingly erratic behaviour.

While there's nothing per se wrong with your code there are a few areas where it could be improved. Here's an alternative version (which also avoids the warning by not opening a file as STDOUT, which I consider bad practice):

sub vpenv {
  my $file = shift;
  open(my $readf,"<","$file") or die "Unable to open file: $!";
  my @stuff=<$readf>;
  close($readf);

  $stuff[0]="setenv DSCUSTOMER $db\n";
  $stuff[1]="setenv DSSITENO $sno\n";
  $stuff[2]="setenv DSCUSTID $sid\n";

  open (my $writef,">","$file") or die "Unable to Write to file: $!";
  print $writef @stuff;
  close($writef);
}

#Updates database.form
sub vpdb {
  my $file = shift;
  open(my $readf,"<","$file") or die "Unable to Open File: $!";
  my @thing=<$readf>;
  close($readf);

  $thing[0]=".ARG DATABASE $db\n";

  open(my $writef,">",$file") or die "Unable to Write to File: $!";
  print $writef @thing;
  close($writef);
}

vpenv("$location/$dir/$site/$vpfile");
vpdb("$location/$dir/$site/$vpdir/$vpdata");
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Or, even better, using Tie::File:

use Tie::File;
sub vpenv {
  my $file = shift;
  tie my @stuff, 'Tie::File', $file or die "Unable to tie $file: $!";
  $stuff[0]="setenv DSCUSTOMER $db\n";
  $stuff[1]="setenv DSSITENO $sno\n";
  $stuff[2]="setenv DSCUSTID $sid\n";
  untie @stuff;
} 

sub vpdb {
  my $file = shift;
  tie my @thing, 'Tie::File', $file or die "Unable to tie $file: $!";
  $thing[0]=".ARG DATABASE $db\n";
  untie @thing;
}

vpenv("$location/$dir/$site/$vpfile");
vpdb("$location/$dir/$site/$vpdir/$vpdata");
[download]