Hive: Best way to do incremetal updates on a main table

If merge in ACID mode is not applicable, then it’s possible to update using FULL OUTER JOIN or using UNION ALL + row_number.
To find all entries that will be updated you can join increment data with old data:

insert overwrite target_data [partition() if applicable]
SELECT
  --select new if exists, old if not exists
  case when i.PK is not null then i.PK   else t.PK   end as PK,
  case when i.PK is not null then i.COL1 else t.COL1 end as COL1,
  ... 
  case when i.PK is not null then i.COL_n else t.COL_n end as COL_n
  FROM 
      target_data t --restrict partitions if applicable
      FULL JOIN increment_data i on (t.PK=i.PK); 

It’s possible to optimize this by restricting partitions in target_data that will be overwritten and joined using WHERE partition_col in (select distinct partition_col from increment_data) or pass partition list if possible as a parameter and use in the where clause, it will work even faster.

Also if you want to update all columns with new data, you can apply this solution with UNION ALL+row_number(), it works faster than full join: https://stackoverflow.com/a/44755825/2700344