When using CDC with incremental + dedupe. is the final table affected if you infrequently delete the SCD table? AFAIK i don’t believe the final table should be incorrect. it contains only active rows, the SCD table contains a history including the which row is active. the binlog position is still maintained internally.

Yes, airbyte stores state and metadata in its own database, either in the docker deploy or some external db you've set up. You can remove the scd table.