with my_jsonb_table as (
  select unnest(array['[[], [1, 2], [3]]'::jsonb, '[[4, 5], [6], []]'::jsonb]) as val
)
select (select array_agg(values)
        from jsonb_array_elements(my_jsonb_table.val) as elements
        cross join jsonb_array_elements(elements) as values)
from my_jsonb_table;



 array_agg 
-----------
 {1,2,3}
 {4,5,6}
(2 rows)

with
  tr_data as (
               select unnest(array['[[], [1, 2], [3]]'::jsonb, '[[4,5],[6],[]]'::jsonb]) as mm
       ),
   unn1 as (
             select jsonb_array_elements(mm) as n, row_number() over() vv
         from tr_data a),
   unn2 as (
             select jsonb_array_elements(n) as n, vv
         from unn1 a)   
select vv, array_agg(n)::jsonb[]
  from unn2 group by vv;