Unfortunately I have encountered a similar issue in the past. To be honest, there is no “quick fix” here. Since bank and credit card accounts have balances that carry over from one year to the next, you only have two options here:
Option #1 – Start a whole new QBO company file as of January 1, 2017. We are only 2 1/2 months into the year and you can easily connect all bank and credit card accounts to QBO and download all transactions as of January 1st and reconcile each month. Check out our how to reconcile a bank account video tutorial which also includes some great troubleshooting tips here:https://fitsmallbusiness.com/bank-reconciliation-quickbooks-online/. Here is the link to how to reconcile a credit card account: https://fitsmallbusiness.com/reconcile-business-credit-card-accounts/.
Option #2 – Take a look at the December 2016 bank statement for all credit card and bank accounts. Take each statement and compare the balance on your 12/31/16 statement to what you have in QBO as of 12/31/16. Whatever that difference is, book a journal entry to “adjust” each account to the correct total.
If you work with a CPA or tax professional then you need to seek their advice before you do anything. I’m assuming that he/she has filed tax returns using the data in your QBO file so you want to make sure that if you go with option #2, they sign off on the adjustments.
Good luck to you and thanks for reading!