If that (update: oops... I meant to reply to that node) works for you, try this as a simplification (untested):

$input_text =~ s{
    ^ ([#]{2,5}) \s+ [^\n]+ \s+ (?= ^ \1 [^#])
    }
    {}xmsg;
[download]

Beyond that, I have to say I don't understand your requirements. Can you express them more clearly?