Try this. It passes your test case :)
#!/usr/bin/perl
# https://perlmonks.org/?node_id=1232492
use strict;
use warnings;
$_ = do { local $/; <DATA> };
my @del =map /^(?=(\d+)\n)(?=.*^bar\n)/ms, /^begin\n(.*?)^end\n/gms;
my $pattern = do { local $" = '|'; qr/^\s+(foo )?ref (@del)\n/mn };
s/$pattern//gm;
print;
__DATA__
ref 1
ref 2
ref 3
ref 4
begin
1
end
begin
2
bar
end
begin
3
end
begin
4
bar
end
ref 5
foo ref 6
ref 7
begin
5
end
begin
6
bar
end
begin
7
bar
end
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