# create a "cache": "is this a NETID?"
# (if I understand your variables correctly...)
my %ids = map { $_ => 1 } values %totalnetname;
my %ECLDATA = ();
{ # lexical scope for leftovers 
 my @leftovers = ();
 while (my $entry = shift @ECL_STAT)
 {
	# ignore non-|-delimited lines
	next unless my ($netid) = split /\|/, $_;
	# push lines which begin with any NETID
	push ( $ids{$netid}
               ? @{ $ECLDATA{$netid} }
               : @leftovers ), $_;
 }
 @ECL_STAT = @leftovers;
}
for my $key (@totalkeys)
{
   my $NETID = $totalnetname{$key};
   my @ECLDATA = @{ $ECLDATA{$NETID} };
   # ... lots, as before.
}