My initial import using "Connect to Square" (entire FY) has multiple discrepancies in each month (no noticeable trend). Is there any way to re-synch the data?

Welcome to the Community, Scott. Thanks for reaching out to us.

Downloaded transactions won't always show the same in QuickBooks Online because it depends on the bank their using. Moreover, duplicate transactions typically occur when banks feed downloaded transactions twice by error. In your case, duplicates will be added to QuickBooks online if you manually import transactions while there are already transactions from the automatic download. 

I recommend excluding duplicate transactions before doing the reconciliation process. It will make it easier for you to reconcile an account. Here's how:

1. Go to the Banking tab, then select Bank transactions.
2. Select the For Review tab.
3. Click the checkbox of the transactions to exclude.
4. Select Exclude.

To read more details about excluding transactions, please visit this article: Exclude a bank transaction you downloaded into QuickBooks Online.

Once completed, you can begin reconciling your accounts to ensure they consistently match your credit card and bank statements.

I've also included this article to learn how to review your beginning balance and look for issues for accounts you haven't reconciled before: Fix issues the first time you reconcile an account in QuickBooks Online.

If you have any additional queries or concerns regarding your bank transactions and the reconciliation process, please get back to us again. We're always available to assist you. Take care!