QB Issue Resolution:

It is not impossible to track down every transaction. Time consuming, yes, but never impossible.

You either spent $16,000 more than you recorded or recorded that much more in income. If it is outflow it should not be that difficult to match up for month 1 the transactions in QuickBooks against the statement. What is left are the items to add. You can get images from the bank for checks you did not enter to enter them now with their correct date. Then month 2, leave uncleared as uncleared and clear the added items that are on the statement.

If you showed too much in deposits you just don’t clear the ones not on the statement. Or edit each deposit to be correct. If you posted, say deposits in month 1 of $90000 but it was only $85000 Then however the deposit was classified made your book balance higher and that is where you adjust.Once you get through to fiscal year end you can make an adjusting expense for that year.

Your tax CPA can tell you if amending returns is even financially prudent. If they charge more than the tax savings it isn’t worth it. You can go back 3 years, I believe, and certain losses can be carried forward

Resolution for Issue 'I’m reconciling an account that has not been reconciled in over 2 years. It’d be impossible to track down every transaction. Is reconciliations discrepancy account okay? After trying to go back and reconcile the accounts, we’ve found that it’s going to be impossible to match every deposit or payment to each invoice or bill. The end of year discrepancy is about $16,000.00 and we’ve already filed our taxes (start up company with a huge loss, filing an amendment would show an even bigger loss). The thought right now is to use an “Other Expenses Account” titled something along the lines of “Legacy Finance Adjustment”, we’d post each months discrepancy against this account so things balance out. Thus it wouldn’t affect our tax reporting, but it would at least get our books in better shape and allow for a reconciliation match….Is this a viable solution? It seems like the only one.' available: Yes (Solved).
Source: Intuit Community forum.

I’m reconciling an account that has not been reconciled in over 2 years. It’d be impossible to track down every transaction. Is reconciliations discrepancy account okay? After trying to go back and reconcile the accounts, we’ve found that it’s going to be impossible to match every deposit or payment to each invoice or bill. The end of year discrepancy is about $16,000.00 and we’ve already filed our taxes (start up company with a huge loss, filing an amendment would show an even bigger loss). The thought right now is to use an “Other Expenses Account” titled something along the lines of “Legacy Finance Adjustment”, we’d post each months discrepancy against this account so things balance out. Thus it wouldn’t affect our tax reporting, but it would at least get our books in better shape and allow for a reconciliation match….Is this a viable solution? It seems like the only one.: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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