You ought not have got a blank target file. However there was a bug in the code. $_-[0] in the regular expression should have been $_->[0].

For test purposes it is conventient to use a __DATA__ section following the code and to print to the console. A test version of the code is:

use strict;
use warnings;

my @pairs = (
    ['WORKING -STORAGE SECTION.', 'declare'],
    ['PROGRAM -BEGIN.', 'begin;'],
    ['^DISPLAY', 'PUT'],
    ['^ACCEPT', 'GET'],
    ['PROGRAM -DONE.', 'END;'],
    );


while (defined (my $line = <DATA>)) {
    $line =~ s/$_->[0]/$_->[1]/ for @pairs;
    print $line;
}

__DATA__
WORKING -STORAGE SECTION.
PROGRAM -BEGIN.
DISPLAY
ACCEPT
PROGRAM -DONE.
this DISPLAY not changed
this ACCEPT not changed
this PROGRAM -DONE. should get fixed
[download]

Prints:

declare
begin;
PUT
GET
END;
this DISPLAY not changed
this ACCEPT not changed
this END; should get fixed
[download]