When using Apsona's deduping tool you may see an option to use "Salesforce API" or "Custom API". This document provides more detail, but in short:
- Use the Salesforce API whenever it is available. It should be an option if you are deduping Accounts, Contacts, or Leads. If deduping another standard or custom object, Salesforce API will not be an option because there is no Salesforce API for any other objects.
- NOTE: that when reparenting related records while using the Custom API, certain field types can cause errors. See this article for more details.