How an R-tree index internally handles null values
If you insert a null value into a spatial column on which you created an R-tree index, the index ignores the insertion and does not create a reference back to the row in the table. Similarly, if you delete a null value from the table, the R-tree index ignores the deletion and the index is not changed, because no reference back to the table row ever existed.
If you update a null value in the table to a non-null value, the R-tree index ignores the deletion of the null value and inserts the non-null value into the R-tree index. Similarly, if you update a non-null value to a null value, the R-tree index deletes the non-null value from the R-tree index and ignores the insertion of the null value.