it gives me an error of uninitialized value in $confID and $confPIN

Generally, you can use defined to test whether a variable holds a defined (initialized) value.

And depending on what you want to happen in that case, you could either skip the rest of the loop body

while (<CONF_ID>){
   my ($confID, $confPIN) = split ' ';
   next unless defined $confID;
   ...
}
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or set the variables to some defined but empty value, e.g.

while (<CONF_ID>){
   my ($confID, $confPIN) = split ' ';
   $confID = '' unless defined $confID;
   ...
}
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just in case you wanted to substitute XXXXXX with nothing, etc., when there's an empty line in CONF_ID...