#!/usr/bin/perl

while (<DATA>)
{
  s/^ ~ .*? \K  _  /+/x;

  print "$_";
}

__DATA__
A line with an_underscore.
A line with_two_underscores.
~A line with an_underscore starting with a tilde.
~A line with_two_underscores starting with a tilde.

##</code><code>##

A line with an_underscore.
A line with_two_underscores.
~A line with an+underscore starting with a tilde.
~A line with+two_underscores starting with a tilde.

##</code><code>##

  s/( ^ ~ .*? )  _  /$1+/xg;