Honest Scope
What a cleanup can and cannot undo
Be clear-eyed about what you are dealing with. If your Undeposited Funds balance is large and old, some of it almost certainly inflated income in years you have already filed. Clearing it now reduces income in the current year, which is a real tax consequence and needs to be a deliberate decision made with your tax preparer, not a side effect of a journal entry somebody posted on a Friday. Anyone who offers to zero out two years of Undeposited Funds without that conversation is doing you a disservice.
There is also a limit to what can be reconstructed. Where payment detail was never exported, where batches were deleted, or where the QuickBooks file has been through a condense, the underlying detail may simply not exist anymore. In that case the honest answer is to quantify the balance, document what it represents as precisely as the surviving evidence allows, clear it with a supported entry, and make sure the process going forward is airtight. That is a legitimate outcome, and it is a very different thing from pretending the number was always right.
What is quick, and worth doing this week regardless of what you decide about the history: the merchant clearing account, the batching by payment type, the fee expense line, and one person owning the deposit step. That combination stops the balance growing immediately, and it makes everything after it possible.
The rest is our ServiceTitan and QuickBooks cleanup. We age the balance, sort it into what is real and what is phantom, correct the open periods properly rather than with a plug, and hand you a file where the bank reconciles without anyone forcing it. If the payments are also arriving before their invoices, you likely have negative accounts receivable at the same time, and if the deposits themselves will not tie, start with deposits that do not match the bank. For setup, see the ServiceTitan and QuickBooks integration or the ServiceTitan resource hub.