Check if update can be changed to left outer join of insert script of table A. Updates are usually heavy compared to Inserts.
See if table is SET table ,on doing updates it might have to scan through other rows to check for duplicate rows.Make it multiset if feasible.
Check data types of primary indexes try and align them.
Collect stats on PI for both the tables.
If they are varchar fields with huge limit try to see alternatives liek using integers.
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