Not an answer, just a comment. Do I get it right:

• "setter" (in quotes, because I understand it's not really a setter) accepts a compiled regex, one you build with the qr operator;
• "getter" returns not this compiled regex, but, somehow, Perl source code fragment, literal string 'qr/.*uba$/i'. Which you then are trying to parse. Or, where does this 'qr/.*uba$/i' come from, and why is it necessary to manually parse Perl expression?

It doesn't make much sense to me, but I haven't worked with MongoDB, hence not an answer, but a promised comment. The reason you get an undef in OP, is because $re are 2 separate lexical variables, 1 per each own small block. They are declared with my and destroyed at closing curly bracket. What's assigned to $_[0], in next line, is presumably global, completely different $re, and undefined at that time. You don't use strict;, do you? I think this change

my $re;
if($2 eq 'i'){
    $re = qr/$_[0]/i;
}else{
    $re = qr/$_[0]/;
}
$_[0] =$re;
[download]

would give you the result you were hoping for.

Edit: Fixed numeric comparison operator to string comparison eq (thanks, poj).