All such insert/update/delete bulk operations need to be batched. What I do (and this is something I am doing many times a year) is something like:

use constant (SYBBATCHSIZE => 1000,
              # ...
             );

# ...

while( for ( my $i = 0; $i <= $#keys; $i += SYBBATCHSIZE ) {
    SqlSub( 'DELETE FROM mytable '
          . 'where pkcol in ( "'
          . join( '", "', @keys[ $i ..SYBBATCHSIZE ] ) . '" )' );
}
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