Yes, deduplication in sync modes does increase the time a sync takes. Here's why:
Deduplication Adds Processing Overhead
How it works: In modes like
Incremental Append + Deduped or
Full Refresh Overwrite + Deduped, Airbyte must sort records by cursor field and identify the latest row per primary key, removing older duplicates. This extra processing step takes time and compute resources. [
Sync Modes Docs]
Warehouse compute costs: Typing and deduplication can increase your destination's compute costs, which scale with the amount of data being transformed. [
Typing & Deduping]
Real-World Examples of Slowdowns •
Full table scans: With CDC Incremental Dedup on a large Postgres → Redshift sync, the normalization phase scanned the entire SCD table (500M rows) on every sync, even when there were no changes — taking hours per sync. [
Forum: CDC Dedup]
•
Query planner degradation: A change in the Redshift destination connector (v4.0.4) caused dedup JOIN predicates to fall back from hash joins to nested loops, turning a 2-minute sync into a 17–43+ minute sync. [
GitHub Issue]
•
ClickHouse behavior: For ClickHouse specifically, the dedup cost is paid
asynchronously by background merges (so syncs themselves are faster), whereas most other destinations pay the dedup cost
synchronously during each sync. [
ClickHouse Docs]
Summary The trade-off is that deduplication gives you a clean, unique-per-primary-key final table, but at the cost of additional sync time and warehouse compute. 👍 0 button 👎 0 button ℹ️
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