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Seems like you are reading Source A table and combining that with processed table B. In that case I would say simple overwrite the result in B and combine Table A and B all the time in glue job.
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In that case I would have to process the entire table B all the time in order not to loose any records (e.g. that are not in the currently processed batch due to bookmarking). For large tables B that does not sound very efficient to me.