If retention is enabled on table-manager -table-manager.retention-deletes-enabled & -table-manager.retention-period=<>, table manager tries to delete all tables in DynamoDB if the retention criterion is met irrespective of the prefixes (set by -dynamodb.chunk-table.prefix=cortex_chunks_ & -dynamodb.periodic-table.prefix=cortex_weekly_).
Issue is the logic here will always create a v1 schema config (if you're using legacy schema based on CLI args) whose ChunkTables PeriodConfig prefix is never set.
Then the table manager code tries to prefix match for an empty string which always matches and all DynamoDB tables get added to the toDelete list.