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Auto-skip is one of the options you will see when creating Scheduled transactions. Please note that you will only see this option if the account you've picked for your Scheduled transaction is connected to Online Banking.
Auto-skip should not be confused with auto-pay.
Creating Scheduled transactions makes sense even if you have connected the account to Online Banking. It's explained in more detail here.
But with transactions coming to your Account register from Online Banking sync and Scheduled transactions creating transactions automatically as they become due, how does MoneyWiz prevent duplicates from appearing? The answer is auto-skip.
When a Scheduled transaction with auto-skip enabled becomes due it'll check if the transaction is downloaded already. It checks it by looking for a transaction with exactly the same amount and transaction date within 3 days (either way - to account for weekends).
If it finds one, it will not post the duplicate transaction but will update the downloaded one with information from Scheduled transaction if necessary.
If it does not find one, it will post the Scheduled transaction in order to make your balance correct. Later, when MoneyWiz will be downloading Online Banking transaction, it'll look for duplicates using the same rules as above.
Therefore the only way a duplicate might appear as a result of this is if your date is not within 3 days period or the amount is not exactly the same. If you are frequently seeing duplicates as a result of auto-skip feature, your transactions probably miss the conditions specified above. In that case, you might be better off with auto-skip disabled. In this setup, MoneyWiz will not pay or skip the transaction automatically - it'll just leave it with a red badge when it becomes due. You can then skip the transaction manually.