In order to be able to return back to the top of the hash, you have to include the top reference to the arguments.

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

use Data::Dumper;

sub insert {
    my ($top, $ref, $head, @tail) = @_;
    return unless @tail;

    if ('break' eq $head) {
        insert($top, $top, @tail);

   } else {
       # Don't overwrite existing paths.
       $ref->{$head} = {} unless exists $ref->{$head};
       insert($top, $ref->{$head}, @tail);
    }
}


my %hash;
while (<DATA>) {
    chomp;
    # Add a dummy end not to throw the last entry away.
    insert(\%hash, \%hash, split(m=/=), '/.');
}
print "\nDump\n", Dumper(\%hash);

__DATA__
f1/f2/f3/f4/break/f1/f2/f5/break/f1/f2/f6
[download]

See also Data::Diver.

Update: Data::Diver example added.

while (<DATA>) {
    chomp;
    for my $path (split m=/break/=) {
        DiveVal(\%hash, split m=/=, $path);
    }
}
[download]