It's a far to general question to be answered easily, could you show us some code?

> # I leave the if statements but then when you call a sub you can't really tell what it will return. As it can vary depending on what if's it might match.

I would suggest to write a wrapper¹ to this legacy code, controlling the state of these global flags

sub wrap_render {
  local $x=shift;
  local $y=shift;
  if ($var) {
    return "your change";
  } else
    return render();
  }
}
[download]

like this you have full control about this "alien" function.

As a general principle I prefer code to be easily understandable and avoid to clutter it with if statements which eventually turns the flow into a labyrinth. Furthermore I try to localize global vars as tight as possible.

So instead of something like

sub render_a {
  print "<a ";
  print "style='$css'" if $global_css_flag;
  print ">"
}
[download]

I would write something like

sub render_a {
  my $style=get_css();
  print "<a $style>";
}
 
{ my $css_flag;
  sub get_css {
    return "style='$css'" if $css_flag;
  }
  sub css_flag { if (@_) {$css_flag=shift} else {$css_flag} }  # gette
+r-setter
}
[download]

(untested)

UPDATE: added checking of new flag $var.

¹) in perl you can give the wrapper the same function name like the wrapped function you're calling from within! Just ask if you wanna go this way!