To improve data encoding for Amazon Redshift tables where sub-optimal encoding has been applied, the correct approach is to analyze the table to determine the optimal encoding based on the data distribution and characteristics.

Option B: Run the ANALYZE COMPRESSION command against the identified tables. Manually update the compression encoding of columns based on the output of the command.The ANALYZE COMPRESSION command in Amazon Redshift analyzes the columnar data and suggests the best compression encoding for each column. The output provides recommendations for changing the current encoding to improve storage efficiency and query performance. After analyzing, you can manually apply the recommended encoding to the columns.

Option A (ANALYZE command) is incorrect because it is primarily used to update statistics on tables, not to analyze or suggest compression encoding.

Options C and D (VACUUM commands) deal with reclaiming disk space and reorganizing data, not optimizing compression encoding.