To illustrate dave_the_m's and Bob9000's point, compare

#!/usr/bin/perl
$Yakkity::Yak::a = 42;
print "a = $Yakkity::Yak::a\n";
print "Undeffing symbol table\n";
undef %Yakkity::Yak::;
print "a = $Yakkity::Yak::a\n";
__END__
a = 42
Undeffing symbol table
a = 42
[download]

with

#!/usr/bin/perl
$Yakkity::Yak::a = 42;
print "a = $Yakkity::Yak::a\n";
print "Undeffing symbol table\n";
undef %Yakkity::Yak::;
print "a = ${'Yakkity::Yak::a'}\n";  # <- Hardcoded reference removed
__END__
a = 42
Undeffing symbol table
a =
[download]

The last reference to $Yakkity::Yak::a keeps the symbol alive. If the reference to one built at run-time, the symbol disappears along with the table.

Sorry, this post just explains what is seen, not how to work around it. Hopefully, someone has a solution.