Do you mean linked at the bank so you can have one Login to access all the accounts? If you're an LLC or S-Corp where everything runs through your taxes anyway, it should not matter at all. If it's an LLP or a S-Corp with multiple owners, then you want to go to your Bank and have them separate the Accounts. One User ID for the Business and a different User ID for the Personal. It would be kind of hard to tell an equal Partner they can't have access to the Bank because your Personal accounts are connected.
And even if you're the sole owner, you do not want to show your Personal Acct in QBs!! (Different than if you can log into the Bank and see everything there.) You only want to show your Business Accounts in QBs. If you do have your Personal Accts in QBs you may want to have a conversation with your CPA/Tax Accountant on how they want you to handle it. You can't really just Delete a QBs Acct if it has any transactions in it, you can only make it Inactive or Hide it. And the numbers from those Accts still show up in some Reports. Your Accountant may not have a problem with this and may just make a Journal Entry to make the Year End numbers look correct.
But to truly have clean books, you'd want to remove the Transactions and then you can Delete the Personal Accts. That would be a royal pain, so check with your Accountant first.
