#!/usr/bin/perl

use strict; # https://perlmonks.org/?node_id=11119658
use warnings;

$_ = <<END;
## This gets stripped

## This doesn't
Because it contains this line

## More headers
blah blah

## this also should be stripped ?

## This should not get stripped, but it does

### This should prevent it from getting stripped, but it doesn't
stuff

#### This should also not get stripped

##### But it does
isn't some text needed here?
END

s/^(#+).*\n\n(?!^\1#)//gm;

print;
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Outputs:

## This doesn't
Because it contains this line

## More headers
blah blah

## This should not get stripped, but it does

### This should prevent it from getting stripped, but it doesn't
stuff

#### This should also not get stripped

##### But it does
isn't some text needed here?
[download]

I think a larger test case may be needed...