Untested, but instead of this:

my @dates_copy = @dates;
while (<NOTES>) {
    $/ = "\n\n";
    my $date = shift @dates_copy;
    push @notes, ($date, $_);
    %notes = @notes;
}
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ponder this:

local $/ = "\n\n";
@notes{ @dates } = map { chomp; $_ } <NOTES>;
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