We have 3rd party app Revel sync with QBO. We have experienced an anomaly with the deposits duplicating — one in the revenue income account and the other in the Undeposited Funds account. How to resolve this?

Yes, I heard this is a known issue and they have not been to resolve this. One word is to create a Revel Adjustments account and write a journal entry removing the entry for the revenue income account and at the year-end, let your Accountant handle this Journal Entry. This way the Undeposited Funds account is left alone.