If the file is written without binmode, it will have been corrupted and will likely be irrecoverable. Simply re-opening the file and stripping newlines is unlikely to work as the binary file may have containd some binary data which looks like newlines, and you would be stripping these too.

getstore doesn't allow you to pass in an open filehandle, but internally, getstore is implemented using LWP::UserAgent::request( url, $file ); and one of it's options is to allow the second parameter to be a callback address (See: LWP::USerAgent::Get() POD; ':content_cb' parameter.).

This allows a simple work around of passing in an anonymous sub that prints the content to a pre-opened, binmode'd output file:

#! perl -slw
use strict;
use LWP::Simple;

open my $fh, '> :raw', $ARGV[ 1 ] or die $!;

my $code = getstore( $ARGV[ 0 ], sub { print $fh $_[ 0 ]; } );

close $fh;

print "rc=$code";
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Note: I've used :raw', rather than binmode, but the effect is the same.