because $1, $2, $3 ... are dynamically scoped to the current BLOCK.
see perlvar

$_ = "aaaabbbbcccc";
if ( not /^(\w\w)(\w\w)(\w\w)$/ ) {
    # inside a block
    if ( not /^(\w\w)\w\w(\w\w)\w\w(\w\w)\w\w$/ ) {
        die "failed";
    }
    print "inside: $_ = $1 $2 $3\n";
}
#outside a block
print "outside: $_ = $1 $2 $3\n";
[download]

The scope of $<digit> (and
$`, $&, and $') extends to the end of the enclosing BLOCK
or eval string, or to the next successful pattern match,
whichever comes first.
[download]

So, in your case, I think inner $<digit> vars go out of scope, getting undef

$_ = "aaaabbbbcccc";
if ( not /^(\w\w)(\w\w)(\w\w)$/ and  not /^(\w\w)\w\w(\w\w)\w\w(\w\w)\
+w\w$/ ) {
    die "failed";
}
print "$_ = $1 $2 $3\n";
[download]

No this still won't work because $1,$2,$3 still fall out of scope because they are not in the 'if' block.
Update: This does work, but don't understand why since the vars have gone out of scope.

They haven't gone out of scope. Here's an attempt at explaining that:

In the first example, you have two if blocks, the first if block provides a new scope for the second block, so what you have is something like this:

# provided by the outermost if
$1 = undef;
$2 = undef;
$3 = undef;
{ # provided by the inner if
   $1 = 'aa';
   $2 = 'bb';
   $3 = 'cc';
}
[download]

Note that one if block will not kill the $<digit> vars, but once the inner block finishes, then its variables are destroyed, and you get the outer block's $<digit>s

Here's an example that might explain it better:

$_ = "aabbccdd";
if ( /^(\w\w)\w\w(\w\w)\w\w$/ ) {
    if ( /^\w\w(\w\w)\w\w(\w\w)$/ ) {
        print "inner: $1 $2\n";
    }
    print "mid: $1 $2\n"; # the inner if's vars are still accessible h
+ere
}
print "outer: $1 $2\n";
[download]

This will print aa cc and not your expected bb dd in the outer block.

Update: here's another way to think of it:

$_ = "aabbccdd";
/^(\w\w)\w\w(\w\w)\w\w$/;
{
    /^\w\w(\w\w)\w\w(\w\w)$/;
    {
        print "inner: $1 $2\n";
    }
    print "mid: $1 $2\n";
}
print "outer: $1 $2\n";
[download]

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