It is part of the QBDT to QBO import limitations process, they forgot to mention it.
Here is my take on how to solve it in QBO?
If you still have access to QuickBooks desktop file, print bank reconciliations report (preferably for the last three months for record).
Let’s say you have done reconciliation through July 31, 2014 in desktop. Reconciliation report should show outstanding checks (under Checks and Payments) as well as deposits in transit (under Deposits and Other Credits).
In QBO for one-time only, do the bank reconciliation through July 31, 2014 again for the same period.
Enter ending balance as of July 31, 2014. Opening balance probably will not make sense, leave it as it is for now. Focus on ending balance.
Select checkbox > Hide transactions after the statement’s end date (upper corner)
Select “ALL” checkbox under Checks and Payments heading or next to Date column
Select “ALL” checkbox under Deposits and Other Credits or next to Date column
Uncheck Outstanding Checks (one by one) based on printed Bank Reconciliation report generated from desktop
Uncheck Deposits in Transit (one by one) based on printed Bank Reconciliation report generated from desktop
Difference should 0 (zero) now.
Select blue “Finish Now” button
Next reconciliation should be part of QBO process now.