Instead of going the /e way, which is a bit hard to read, I'd remove the offending part from the string, do the replacements, and return it back:

#!/usr/bin/perl
use warnings;
use strict;

use Test::More tests => 4;

sub fill {
    my $_ = shift;
    my $prefix = do { s/^(-*B?)// ; $1 };
    1 while s/-B/BB/g or s/B-/BB/g;
    return "$prefix$_"
}

is(fill('--------NNNNNNN--------NNNNN--------NNNNN------NNNNNNN-------
+------BBBBB-----'),
        '--------NNNNNNN--------NNNNN--------NNNNN------NNNNNNNBBBBBBB
+BBBBBBBBBBBBBBBB',
   'test1');

is(fill('---------NNNNN-NNNNNNNNNNNNN----NNNNNNNNNNN---------BBBBBBBBB
+B'),
        '---------NNNNN-NNNNNNNNNNNNN----NNNNNNNNNNNBBBBBBBBBBBBBBBBBB
+B',
   'test2');

is(fill('-------NNNNNNN-----------------BBBBBBBBBBBBBBB-------------NN
+NNNNN'),
        '-------NNNNNNNBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBNN
+NNNNN',
   'test3');

is(fill('--------BBBBBBBBBBBB-------NNNNNNNNNNNNN------NNNNNN'),
        '--------BBBBBBBBBBBBBBBBBBBNNNNNNNNNNNNN------NNNNNN',
   'test4');
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