Another approach using split and join: 
#!/usr/bin/env perl
use strict;
use warnings;

foreach my $file (grep { -f } @ARGV) {
    my $data = slurp_file ($file);
    my $new_data = join ('', (split /(SIL\n)/, $data, 5)[ 0 .. 3 ]);
    open my $OUT, '>', $file or die $!;
    print $OUT $new_data;
    close $OUT;
}

sub slurp_file { local (*ARGV, $/); @ARGV = shift; <> }

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Update

This only works if there are no additional SIL lines interspersed between the first line and the SILL lines at the end.

In reply to Re: removing lines that are in the end of a file by gsiems
in thread removing lines that are in the end of a file by bhargavkanakiya

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