Yes, you can reconcile the account normally even if both the opening and ending balances are 0.00.
Enter the statement ending balance as 0.00 and reconcile the transactions for the period against the Bank Account Ledger Entries in Business Central.
With a daily sweep, the important thing is that the sweep transactions are also recorded in BC. For example, a 10,000 deposit followed by a 10,000 sweep will leave the account at 0.00, but both transactions still need to be reconciled.
So the key is to reconcile the transactions, not the balance. If the sweep entries aren't in BC, those will likely be the items causing the difference.
Thanks, Sanket