If $dir/$new already exists, you do not rename it. That's not what I think you want. What about this:
sub fixdir {
my $dir = shift;
opendir my $DH, $dir or die "Cannot open '$dir': $!";
while (my $f = readdir $DH) {
next if grep $_ eq $f, qw/. ../;
(my $new = $f) =~ s/[^a-zA-Z0-9_.]/_/g;
if ($new ne $f) {
$new .= '1' while -e "$dir/$new";
print STDERR "Renaming: $f -> $new\n";
rename "$dir/$f", "$dir/$new";
}
fixdir("$dir/$new") if -d "$dir/$new";
}
}
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