You have to buffer each block. You need to know which segments are part of a block and which start a new block. The code will look something like this:

#!perl -w

my ($fs, $cs, $rs, $ec, $ss);
setdelimiters('|^~\&');
sub setdelimiters {
    ($fs, $cs, $rs, $ec, $ss) = map {quotemeta} split //, $_[0];
} 

use strict;

my $buffer="";
my $suppress = 0;
my @field;
my %newblock;
my %partofblock;

# Note: This is just an example.  I do not know all segments that star
+t a new block
$newblock{$_}    = 1 for qw(MSH);
$partofblock{$_} = 1 for qw(EVN PID PV1 FT1);

while (<>) {
  if (/^(MSH)(.....)/) {
    setdelimiters($2);
  }

  @field = split /$fs/;
  if ($newblock{$field[0]}) {
    processbuffer();
  } elsif (!$partofblock{$field[0]}) {
    print STDERR "Possible error: segment=$field[0] line $.\n";
  }
  if ($field[0] eq "FT1") {
    if ($field[_WHATEVER_] == 123456) {
      $suppress = 1;
    }
  }

  $buffer .= "$_\n";
}
processbuffer();

sub processbuffer {
  print $buffer unless $suppress;
  $buffer="";
  $suppress = 0;
}
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