You are correct.  Bypassing the payables module by unlinking the Accounts Payable account will update the balance sheet balance for that account but will not keep track of who you owe or which vendor your just credited.  Therefore the total of the balance sheet account and the total of what you owe vendors will no longer match and you books will unbalanced when you look at the Data Integrity Check on the Maintenance menu.

Something tells me you might be dealing with year end adjusting journal entries from your accountant.  If this is the case, the reason you are posting the entry is important if there is no vendor attached to the entry.  If you are willing to share the reason for the entry, we may be able to help, otherwise, you should ask your accountant how to post the entry without a vendor (eg. what other account could you use - like Accrued Liabilities).