It sounds to me like you want this, but i'm not really sure?

if( (defined $afile) && !(defined $bfile) )
{
  &parse_recent;
  &parse_monthly;
  &parse_new;
  &create_temp_a;
  &copy_new_to_recent;
  &copy_recent_to_monthly;
  &remove_excess; 
  &done; 
} elsif( (defined $bfile) && !(defined $afile) )
     {
       &parse_recent;
       &parse_monthly;
       &parse_new;
       &create_temp_a;
       &copy_new_to_recent;
       &copy_recent_to_monthly;
       &remove_excess; 
       &done; 
     }
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